In a brief flashback, Edward Elric and Alphonse Elric had attempted to perform an alchemical transmutation in the hopes of bringing their late mother back to life, but they had failed in doing so. As a consequence, Alphonse disappears, Edward loses his left leg, and a grotesque figure appears in the transmutation circle. In the present, the brothers walk across a desert. They arrive at Liore, where they hear about a religious leader named Father Cornello who can create miracles. However, as they realize that he is performing alchemy and ignoring the law of equivalent exchange, they believe that he possesses the philosopher's stone, which they had been searching for to restore Alphonse's body. Threatened, Cornello orders Cray to kill them. Rose, a girl the brothers meet, is traumatized after witnessing Al's lack of a human body, runs to Cornello. Edward and Alphonse follow her, and Cornello releases a chimera on them when they meet. Cornello also transmuted a giant bird from a parrot and sends it to fight against Edward. Edward fends both of the chimera and the bird off by exposing his automail, his metal arm and leg. Cornello then realizes why Edward Elric is nicknamed the Fullmetal Alchemist, understanding that the brothers had committed the ultimate sin of human transmutation.

After revealing that they were trying to revive their mother, Edward and Alphonse warn Rose that reviving her boyfriend Cain would result in a similar fate. Cornello attacks the boys to chase them away, and he later show a silhouette of Cain in order to comfort Rose. He then orders the townspeople to attack and capture the Elrics. Edward transmutes some metal to look like Alphonse, and allows himself to be captured. Cornello then takes the state alchemist pocket-watch from Edward, assuming that it is his secret to performing alchemy without a transmutation circle. Cornello catches Rose trying to visit Cain and he reveals the silhouette to be a chimera made of birds. He leaves her to be eaten by the chimera, but Alphonse arrives just in time to save her. As Cornello tells Edward his plan to use Liore as the base for world domination, Alphonse broadcasts it across town. Edward then defeats Cornello with his superior alchemy, only to find out that the philosopher's stone is a fake. When Rose confronts Edward and Alphonse about how their exposing Cornello did more harm than his deception, Edward tells her to walk on her own two feet. As the Elrics leave, Lust and Gluttony manage to salvage their plans with Liore by killing Cornello and replacing him with Envy masquerading as the real Cornello.

In a flashback that continues through to episode nine, Edward and Alphonse learn alchemy from a very young age, taking after their father, who apparently abandoned his family when Alphonse was still too young to remember him. They show their alchemy to both their friend Winry Rockbell and their mother Trisha Elric. Trisha encourages them in the pursuits of alchemic knowledge, but she dies from a sudden illness and the brothers vow to revive her with alchemy. They apprentice themselves to an unnamed alchemist, and after their training, they attempt to resurrect Trisha. The transmutation goes awry, in which Edward loses his left leg and Alphonse loses his entire body. Edward then sacrifices his right arm to attach his brother's soul to a suit of armour. Alphonse carries Edward's broken bleeding body to Rockbell Automail. Roy Mustang arrives unexpectedly, having received a letter the boys sent to his office, inquiring about their father Van Hohenheim. Having seen the attempted human transmutation, Mustang tries to recruit the boys to become state alchemists, but Pinako Rockbell orders him to leave. Edward pays Pinako for automail limbs and decides to become a state alchemist so that he can gain privileged access to the state library, and find a way to restore Alphonse's body. Edward and Alphonse burn down their childhood home so that in efforts of not giving up and try to return and leave Resembool.

On their way to Central, Edward and Alphonse stop at a train station where they hear of an alchemist named Majhal, whose name had appeared several times in their father's correspondences relating to human transmutation, and decide to pay him a visit in the area. Upon entering Majhal's village, they encounter a girl named Clause, who tells them that a zombie has been murdering several of the villagers, her older sister being one of them. Clause petitions the brothers to avenge her sister's death, but Edward is sceptical of the whole situation. Upon meeting Majhal, he tells the brothers that the mysterious zombie is believed to be his former lover Karin, who died in an accident several years ago. After some more investigation, the brothers discover that Majhal has been attempting to revive Karin by using mannequins that look like her, and using alchemy to attach the souls of the village girls he has kidnapped to the mannequins, kidnapping Clause to use her soul. Edward discovers that Karin had not died, but initially lost her memories and has aged. Once her memories returned, she had sought out Majhal, but he was already too possessed by his passions of reviving Karin to recognize her. Majhal refuses to accept the wrinkled old woman who has been supporting him as his Karin, and he attempts to kill Edward. Edward knocks Majhal's weapon out of his hand, which flies into the air and accidentally impales Majhal, killing him. Clause reverts to dressing femininely and sees the brothers off as they continue on their journey.

Edward and Alphonse are told by Mustang to board the train that is currently leaving the station. Their train is hijacked by a group of terrorists led by a man named Bald. They take General Hakuro and his family captive and demand that their leader is released from prison. However, Edward and Alphonse fight back, and meet Major Maes Hughes, who helps them defeat Bald and rescue Hakuro. The train arrives safely at the station and the military moves in to arrest the terrorists. Bald manages to escape, but Mustang demonstrates his abilities as the Flame Alchemist and restrains Bald. Mustang then informs Edward that the grateful Hakuro has given him special permission to take the state alchemist examination, which surprises and annoys Edward because of the implication that Mustang manipulated him.

Edward and Alphonse begin preparing for the state alchemy examination while lodging with Shou Tucker, known as the Sewing-Life Alchemist, who is credited for creating intelligent chimeras. The brothers become fast friends with his young daughter Nina and her dog Alexander. Hughes and his wife Gracia throw a birthday party for Edward, interrupting a chance to cram. During the party, Gracia goes into labour and they witness the birth of Elicia. Edward discovers at this time that he can perform alchemy without a transmutation circle. After the written portion of the test, Mustang forces Alphonse to drop out due to his absence of a body, and the suspicions that this fact would raise were it to be discovered by his higher-ups. Ed successfully passes the interview and passes the practical portion when he saves the entire prospective state alchemist group with his quick thinking, courage, and ability to transmute without the use of a circle.

Edward is now a dog of the military for having passed the state alchemy examination. Mustang gives Edward a silver pocket watch, being a symbol of his rank and an alchemical amplifier. Edward writes a letter to Winry, and Nina writes one to her mother. After Tucker's reluctance in answering Edward's questions concerning the talking chimera that he created two years ago, Edward investigates at the state library but is denied access. On the way out of the library, Edward encounters a mysterious man with a cross-shaped scar across his face, and a strange tattoo on his right arm. After Brigadier General Basque Grand finds out about Edward's investigations, he orders him to cease and desist, having Edward and Alphonse moving out of Tucker's mansion. However, Edward and Alphonse sneak into the mansion into Tucker's laboratory in the basement, where he has just finished creating another speaking chimera in order to satisfy his yearly examination requirements. Edward then verbally places the pieces of the puzzle together, revealing to Alphonse and the audience that Tucker was responsible for using his wife for his first chimera, and now he is using Nina and Alexander for his new chimera. Tucker tries to accuse Edward that he is guilty of this as well, and Edward nearly beats Tucker to death in response, though is stopped by the Nina-Alexander chimera. As Tucker is arrested, Edward manages to free the chimera, which escapes into an alleyway and encounters the scarred man. He declares it to be a sin against nature, and kills it. The scarred man disappears, and Edward and Alphonse discover Nina-Alexander's blood-smeared remains on the alley wall.

Anguished by the horrible demise of Nina, and disgusted at his first assignment of organizing Tucker's research after learning of the man's death, Edward considers deserting to track down her killer. Luckily, Alphonse finds reference to the philosopher's stone among Tucker's papers. Edward is incredulous that such a thing even exists. Left to his own devices, Alphonse has spoken to Führer King Bradley. Winry, who has arrived at Central to visit, is kidnapped by a butcher-turned-serial killer named Barry the Chopper, who disguises himself as a woman. Edward gets kidnapped and his automail arm taken from him as he tries to free Winry and run away. Forced into a fight for his life, Edward almost kills Barry in an act of maddened desperation until Alphonse arrived to stop him, having the authorities arresting Barry. Edward breaks down in tears, and then agrees to search for the philosopher's stone with Alphonse. Mustang later allows them to search for it, with the caveat that he be kept abreast of developments. Edward is officially dubbed the Fullmetal Alchemist by Bradley.

While Edward and Alphonse take Winry shopping, Edward receives his second assignment to inspect the coal mines at the town of Youswell. However, the townsfolk is distrusting of the state military. Lieutenant Yoki, the military commander in charge of the area, comes to collect taxes from the local inn, though a riot erupts. Edward appears in time before Yoki nearly murders Kyle, the son of the innkeeper. Yoki invites Edward to his mansion, after noticing that the Edward is a state alchemist, through flattery and bribery. The inn is suddenly destroyed come nightfall, in which Alphonse save Kyle from under the rubble. Edward reluctantly transmutes the gold coins that Yoki attempted to bribe him with, overlaying the gold over coal bars. He then uses them to purchase the mine from Yoki under the guise of a priceless transfer before returning the bars to stone and selling the entire town to the people of Youswell for a single night stay at the newly repaired inn. Edward defeats Yoki's alchemist servant Lyra, becoming known as a hero.

After exposing Cornello in Lior as a fraud, Edward and Alphonse are on their way back to report to Mustang about the incident. They stop at the town of Aquroya and get caught up in the manhunt for a talented cat burglar named Psiren, who uses her skills as an alchemist to repeatedly fool the local police. The chief police officer convinces Edward and Alphonse to capture Psiren, yet Psiren tricks them three times for believing that she steals for the good of the people, seemingly saving certain buildings from being torn down. However, Psiren gets away with having a building getting demolished anyway. Alphonse, still believing that Psiren is really a good person, tries to stop Edward from catching Psiren before she gets away with the loot. Edward is later able to catch Psiren, but she still makes an escape. Edward realizes her importance as a draw for tourism in the sinking city of Aquroya.

Edward and Alphonse arrive in Xenotime to look for the philosopher's stone. After they save a young girl named Elisa trapped under a fallen mine cart, she brings them to the tavern out of gratitude. During the feast in their honour, the brothers hear that a philosopher's stone is near completion, researched by a man named Mugiar. It is soon realized that there are impostors they assuming Edward and Alphonse's names. When they sneak into Mugiar's mansion, they are fended off by the older impostor. Alphonse is unable to buy medicine for Elisa, since the townspeople believe that he is one of the impostors, but the younger impostor later appears and buy him the medicine. The following night, while Edward and Alphonse enter the mansion a second time, the older impostor, recognized as Russell Tringham, attacks Edward using crimson water, however the younger impostor, recognized as Fletcher Tringham, saves him, revealing that this water has polluted the town with its toxicity.

A stunned Mugiar, asks the Tringham brothers to find an alternate method to create the crimson stone at a faster rate, but Russell goes against this. As a response, Mugiar captures them for knowing that they are the impostors. Back at the tavern, Edward and Alphonse learn that Nash Tringham, the father of Russell and Fletcher, was the original discoverer of the crimson water, but he soon left the town after a disease was spread from his research. Edward and Alphonse also find out about Tim Marcoh, who treated this deadly disease with a mysterious method. Mugiar invites Edward and Alphonse to do more research on the crimson water. They free Russell and Fletcher and confront Mugiar about Nash. Mugiar tries to attack then, but he is soon overpowered. He escapes underground, but also collapses the passageway, causing the crimson water flood out of the spring. Fletcher uses alchemy to make the trees absorb the water, neutralizing the threat. Edward and Alphonse say farewell to Russell and Fletcher, boarding a train for East City.

Edward and Alphonse report to Mustang regarding about the investigation into the philosopher's stone. Kain Fury picks up a dog and tries to get someone to adopt it but fails. Mustang and Hughes then discusses with Edward about Marcoh. Grand later interrupts and declares that Marcoh was a deserter. When Edward is offered re-certification, he challenges Mustang to a duel in exchange for the information. The approved duel is set to fight in the parade grounds. Mustang nearly defeats Edward, but allows him to counter from his hesitation. Mustang informs Edward about Marcoh after halting the match. That night, Hughes reveals that a man named Scar is responsible for Bradley's move.

Civil unrest has broken out in the town of Lior with Envy using his shape-shifting powers to disguise himself as Cornello. Edward and Alphonse find Marcoh and learn about the usage of the philosopher's stone in the Ishbal rebellion before he went missing. Grand enters with soldiers, confiscates Marcoh's information on the philosopher's stone, and arrests Marcoh, leaving Edward and Alphonse behind. However, Scar appears and kills Grand before turning his attention to Marcoh. Edward, Alphonse, and Marcoh quickly evade into a tunnel, long enough to be saved by Alex Louis Armstrong, the Strong Arm Alchemist.

Armstrong reveals that Scar is an Ishbalan alchemist during their battle. Marcoh tells Edward and Alphonse about the Ishbal massacre, how state alchemists were used against the Ishbalans, who viewed alchemy as heretical. Marcoh, forced to use his research, caused huge casualties on the Ishbalan side. Mustang, forced to kill a pair of doctors, who were saving lives from both sides, allows Marcoh to desert. When the doctors are revealed to be Winry's parents, Marcoh refuses to escape to Resembool with the brothers. Scar, fleeing from the military, runs into Edward and Alphonse again as they defend themselves against him, resulting in Scar destroying Ed's arm and damaging Al's body. Just as Scar prepares to finish off Edward, Marcoh throws his red stone at Scar, causing Scar to painfully absorb the stone into his tattooed arm. Outnumbered by military reinforcements, Scar manages to escape into the sewers and Marcoh is taken to a safe location by the Führer's personal secretary.

Armstrong escorts the Elric brothers back to Resembool to have themselves repaired. Lust attacks Marcoh in his safe house and coerces him into revealing the location of his research on the philosopher's stone. Lust and Gluttony then kill him as they make their way to the state library. On the train to Resembool, Edward and Armstrong discover that Alphonse was unloaded at the previous station and are forced to search for him. When Armstrong urges patience, Edward explodes in rage and abandons Armstrong. However, Edward is soon jumped by a girl who steals his automail leg. The girl's grandfather, while giving back Edward's leg, explains that he lost his leg during the Ishbal rebellion and that he wishes to retain his wound as a reminder of it. Meanwhile, Alphonse is stolen by a boy who wishes to prove himself by raiding an enemy's mansion. Alphonse frightens the boy by claiming he is a haunted armour. Edward and Alphonse reunite as Armstrong reappears. Armstrong grabs them and dashes toward the departing train, hoping to catch it.

Edward, Alphonse, and Armstrong all return to Resembool, meeting up with Pinako, who agrees to repair Edward in three days’ time. While the Elric brothers recuperate, Armstrong assists Winry and Pinako in work. Edward and Alphonse later reminisce about their childhood while at their mother's tombstone. Alphonse seems to worry about having fading memories, but Armstrong breaks the tension. A few days later, receiving his replacement arm and leg, Edward uses his alchemy to rebuild Alphonse's armoured body from the shattered remains. Afterwards, the brothers and Armstrong head back to Central to find Marcoh's research.

In the state library, Lust searches for Marcoh's research before encountering Scar, in which she reminds him of a previous acquaintance. He realizes that Lust and Gluttony are homunculi as the library is sent ablaze from their attack. Edward and Alphonse meet Denny Brosh and Maria Ross, their new bodyguards, not long before their find the first branch of the state library burned to the ground. Edward and Alphonse go on an exhaustive search to find other sources for the book, leading them to Sheska, a file clerk who formerly worked at the library before being fired for reading all the time. Sheska reveals that she has memorized all of Marcoh's works, and then makes handwritten duplicates for the Elric brothers. The writing is written in a code created by Marcoh, though resembling that of a cookbook. The brothers attempt to decipher the hidden data for several days, only to discover that producing the philosopher's stone requires human lives.

Horrified by the key ingredient in making the philosopher's stone, Edward and Alphonse nearly give up their quest. However, Ross inspires them to continue. A hidden piece of information reveals an unused laboratory next to a prison where raw materials for the stone were gathered. Ignoring the orders of Brosh and Ross, they sneak out to investigate the laboratory themselves. Scar attacks the dormitories and gathers that the brothers have travelled to the fifth laboratory before pursuing them. Edward enters the building via an air duct, triggering several traps before finally meeting the security guard named Number 48. Outside, Alphonse is ambushed by another security guard named Number 66.

Edward and Alphonse learn that the guards are souls bound to empty suits of armour. Edward struggles in his battle against Number 48, a serial killer known as Slicer, when his automail arm malfunctions, the result of Winry forgetting to add a small bolt. Edward is troubled to see that his opponent is a pair of brothers, where the younger one controls the body. Edward manages to defeat Slicer by use of Scar's destruction technique, yet he refuses to finish them off, due to seeing Alphonse in the same manner. Alphonse realizes that Number 66 is Barry the Chopper, who tries to suggest that Alphonse never truly existed, saying he was a doll made for Edward. Contemplating on the possibility, Alphonse recalls that Edward was afraid of telling him something.

Scar luckily arrives and helps a disadvantaged Alphonse defeats Barry. This causes Barry to set off explosives, freeing an imprisoned Greed as well as others around him. The older Slicer agrees to take Edward to the interior of the laboratory, but the younger Slicer breaks his blood seal after Edward calls him human. Solf J. Kimblee, the Crimson Alchemist, and several other prisoners are led by a fake Grand to be ingredients for the philosopher's stone. Edward and Slicer are attacked by mutant chimeras until they are called off by Tucker, who, after his death was fabricated, has become a chimera himself. As Alphonse and Scar travel into the laboratory, Scar reminisces about his brother and Ishbal, but they are attacked by Lust and Gluttony, who Scar reveals to be homunculi. Tucker shows Edward around the laboratory, who realizes that he has been given the opportunity to create the philosopher's stone.

Hughes organizes an expedition to rescue Edward and Alphonse in the fifth laboratory. Envy, in the guise of Grand, gathers the human ingredients and forces Edward to attempt to transmute a philosopher's stone. Bradley joins the expedition and mobilizes the military in the rescue mission. Kimblee sets off an explosion, causing the prisoners to fall into the room below. Edward questions the prisoners for their reason being in the laboratory, though this results in a fight against Envy before Lust intervenes. Lust takes Alphonse hostage, giving Edward the ultimatum of transmuting the philosopher's stone or watching Alphonse's blood seal be broken. Edward fails in his struggle to transmute the stone. Suddenly, Edward's body begins to react after being doused in the incomplete stone, destroying his surroundings. The homunculi escape as the military invades the base and Ross calms Edward down.

Edward, recovering from his wounds from the laboratory, is scolded by Ross for almost dying. Needing his automail repaired, Edward calls for Winry to come to Central. When Winry arrives at the train station, Alphonse still contemplates what Barry had told him. After the brothers refuse to tell her about the events, Winry leaves in a fury and is dragged off by Hughes to his daughter's birthday party. Hughes tells her that men tend to hide things so as not to worry anyone. Alphonse decides to confront Edward about what he was afraid to tell him, asking if he was really an artificial soul.

Alphonse has run away after not receiving an answer from Edward. He soon runs into Scar, who has been hiding among other refugees from Ishbal as they are terrorized by mercenaries posing as the state military soldiers with Barry accompanying them. After being reunited with his brother, Edward and Alphonse reaffirm their existence.

Deciding to follow Scar to get clues about the philosopher's stone, the brothers take Winry with them when she notices that Rush Valley, a town best known for its automail shops, is en route. As they leave, Hughes investigates the fifth laboratory, discovering a connection between it and the war in Ishbal. He confronts the key suspect in it, Juliet Douglas, but is then attacked by Lust. He escapes the two women and tries to telephone Mustang with his information via telephone booth, only to be attacked by Envy disguised as Ross before he assumes Gracia's form to deliver the death blow. Hughes is posthumously promoted to the rank of a brigadier general.

Mustang investigates Hughes' murder and concludes through Armstrong that a high ranked member of the military may be responsible for his death. Izumi Curtis, Edward and Alphonse's teacher, shows up at Central looking for them, but she has missed them by a few days. Edward, Alphonse, and Winry, on their way to Ishbal, arrive in Rush Valley.

Izumi has finally caught up with her wayward proteges, Edward and Alphonse. They have every reason to fear her as she drags them back to Dublith.

Izumi strands Edward and Alphonse on Yock Island, where they originally learned an important life lesson before she took them on as apprentice’s years before. She wants them to have time to reflect on their mistakes.

The young boy who shadowed Edward and Alphonse on Yock Island is not only an alchemist, he is able to transmute his own body. After finding out about the scars on the boys right arm and left leg, Ed discovers that the boy is a homunculus who took his limbs during their failed attempt at human alchemy.

Yoki spots Scar in a group of Ishbalans arriving at a refugee camp. He runs off to contact the military, hoping to be reinstated. Meanwhile, the military, believing the mysterious boy to be a homunculus, captures and imprisons him in South Headquarters. A chimera called Bido discovers the same and Izumi storms South Headquarters to rescue him, but she soon finds herself in a five-way fight over the boy.

Amid the confusion inside South Headquarters, Envy, disguised as Bradley, manages to take the homunculus boy from Izumi. Kimblee and Bido came to battle for the same purpose and the boy remembered all his past after he consumed small fragments of the Philosopher's Stone.

Edward and Alphonse battle the new homunculus known as Wrath, who wants the rest of Edward's body to make himself human. Izumi interrupts the fight by separating the combatants with a deep chasm. After Wrath escapes, Izumi sends Edward and Alphonse to meet her alchemy teacher, an old woman named Dante, to learn an important lesson about the principle of equivalent exchange. At Dante's house, they discover that Lyra has become her apprentice, and Greed's party comes and battle Edward and Alphonse.

Marta hops inside Alphonse's armour and slows him down just enough for Loa to overpower Al, and the kidnappers take him to their headquarters for a rendezvous with Greed. While Ed searches through town to discover any information on Al's whereabouts, Izumi goes to see Dante. In an intense conversation, Dante reveals that the kidnappers left an emblem revealing the name of the pub Al has been taken to. At the hideout, Greed reveals to Al that he desires the knowledge of how souls can be bound to inanimate objects, such as Al's suit of armour. Izumi bursts onto the scene to rescue Alphonse from the powerful homunculus and his cohorts, and is later joined by Edward.

They are unable to cause harm to him, however, as he utilizes his Ultimate Shield whenever attacked. Before he and Ed can truly battle, the military bursts into the building to take over. During the escape, Greed discovers that Kimblee has betrayed his team, but has no time to deal with him, as the kidnappers must take Al and leave. Before Ed is able to run after them, he is cornered at gunpoint by the military, whom demand he stand down and report to Lt. Commander Archer.

Frank Archer has Edward as well as Izumi and Sig Curtis in custody. Archer reinstates Tucker as a state alchemist under his command and orders his men to take no prisoners hunting down Greed and his associates. As Greed tries to escape with his cohorts, Strongarm burst through the wall and battles with Law until Law collapses the wall, ensuring the group's escape. While Greed and co. recover in a small shack, Lust and Gluttony appear. Dolcetto and Law unwaveringly step up and sacrifice themselves allowing Greed, Al, and Marta (who is still inside of Al's armour) to escape. In a forest, Greed instructs Al to wait for him until sunrise, and for Marta to watch after him while he goes to take care of business. Marta realizes he is headed for Dante's house and tries to go after him, but Al refuses to allow her to do so.

When Greed arrives at Dante's, he is greeted by Lyra, who knows his purpose for returning to Dante's. She guides him to a parlour, where he discovers Dante's body split down the middle, seemingly by a sword, and a complex alchemy circle on the ceiling and floor. Before he has time to react, Lyra uses alchemy to forcibly eject the Philosopher's Stone fragments that Greed has consumed in his life. She exits, leaving him in pain, as Ed enters. Shocked at Dante's corpse, he blames her death on Greed. While they fight, Ed discovers the secret to his human shield through logic, and uses alchemy to undo it. He manages to stab Greed in through the chest, which surprisingly causes Greed to collapse in pain. Greed explains to Edward that the only way to kill a homunculus without its regeneration is to physically murder one near the human remains that it was created with, and he also reveals that he let Al go. Greed departs this information with Ed in hopes of ensuring the deaths of the rest of the homunculi, and then he dies, much to the shock of Ed who has never killed before. At sunrise, Marta gets up and leaves Al, knowing that Greed isn't returning. The brothers reunite and, together with Winry, Izumi, and Sig, bury Greed and Dante. They bid Izumi and Sig goodbye, saying they will next find the Ishbalans.

Lust, Envy, and Gluttony are in a restaurant discussing Greed's recent death. As they leave, a car wreck outside causes a small boy to become injured. The mother's cry for help brings forth a man who heals him using a ring similar to the one that Cornello wore in Lior. Lust watches the man heal the child, and as he turns to the crowd as sees her, she recognizes him as Lujon, a man from her past. They catch up in the restaurant, where a flashback shows us how Lust and Gluttony watch the results of a landslide and its victims. As they watch, a rescue crew approaches, containing Lujon, and he rescues a girl from the pile. Meanwhile, Ed, Al, and Winry, while riding in a cart south to the Ishbalan camp, must save a girl from a band of thugs in the forest. She reveals her name is Lydia, and that she is looking for a man named Lujon, who is supposed to be finding a second Philosopher's Stone to save the people of their village from the return of a plague. As Lujon, Lust, and Gluttony ride back together to his village, Lujon reveals that the power in his Philosopher's Stone has waned considerably. The flashback continues, revealing how Lujon's failed attempts to cure the first onslaught of the plague provoked Lust into teaching him the refined arts of alchemy. As they study together, Lujon falls in love with her; however, Lust only stays with him because he invokes faint memories in her mind that she cannot identify. Once he has learned the secrets to curing the illness, he manages to save his fiance Lydia from death's grip. On the day of their wedding, Lujon leaves her at the altar for Lust, who unsuccessfully commands her to go to him. Once he leaves, she laughs with Envy about the success of their plan.

In present time, Lujon embraces Lust in the village before saving his people, exclaiming how he won't let her leave him this time. Before he can let her go, Lust stabs him, killing him. The villagers all perish, and minutes later Ed and company arrive to witness the tragedy. Lydia runs into the fog before Ed can stop her, and is found lying dead next to Lujon's corpse, succumbed to the disease as Lust rides away in her carriage.

On their way to Ishbal, Edward and Alphonse try to help a group of Ishbalan refugees being shipped further south by the military, hoping to get more information about the philosopher’s stone and the war in Ishbal.

In this comedy interlude, Jean Havoc has been investigating Mustang under orders from internal affairs, and he enlists several comrades to help. However, Mustang's theft of Havoc's potential girlfriends is negatively affecting Havoc's productivity, so Mustang orders Vato Falman to find Havoc a date. Armstrong recommends his sister, who rejects Havoc because she expected someone more muscular. In the other half of the episode, Mustang is roped by his subordinates into investigating the mystery of the haunted thirteenth warehouse that appears out of nowhere.

After wrecking the tractor that Winry stole for them, Edward and Alphonse have arrived at a town after a long walk. They separate after getting into an alchemy-enhanced argument about what they should do next. Alphonse then bumps into an old acquaintance, Marta. Meanwhile, Winry meets with Sheska in Central, and the two decide to launch their own investigation into the murder of Hughes. They discover what Hughes had discovered about Juliet Douglas, and then eavesdrop on a conversation she has with Envy.

On the train ride to a military base near Lior, Mustang is dismayed to discover that Kimblee is a part of the force and has been reinstated as a state alchemist by Frank Archer, who has been promoted to Colonel for this operation. Marta, Ed, and Al arrive in Ishbal, and are surprised to find that only ruins remain. There, they discover that Breda and Havoc have been spying on them, and they are brought to Mustang, who puts the Elric brothers under his supervision. At dinner, Mustang shows Ed an aerial view of Lior, which reveals that Scar, who has been dragging a giant rock around the city, gouging the earth, is creating a giant Grand Arcanum transmutation circle, which upsets Ed.

Ed then goes to Colonel Archer and asks to go undercover into Lior to investigate the area for the military. Archer agrees on the condition that Al is left behind so Ed does not have the will to go AWOL. He then leaves after giving Armstrong his silver pocket watch.

After arriving in Lior, Ed finds his old acquaintance Rose, who is now called Holy Mother and unable to speak. He also runs into Scar, and the two of them begin battling in an alley, to be interrupted by Lust and Gluttony.

Al and Marta are shocked to find Solf J. Kimblee at the military base, and Marta, acting out of rage, attacks Kimblee, and after a failed attempt to injure Marta by sacrificing a soldier, Kimblee finds himself fighting Al, who is protecting Marta. The battle is broken up by Mustang.

Scar reveals his past to Ed, at the insistence of Rose and Lyra, who is acting as Rose's voice. Before the war, Scar's brother lost his fiance due to a fatal illness, and tried to use alchemy to bring her back, but instead created Lust. His brother then went on to create the Philosopher's Stone, and it is revealed where Scar's tattooed arm comes from, and the X-shaped scar on his face. He then reveals his plans to use the Grand Arcanum to create another Philosopher's Stone, but not by sacrificing the people of Lior, but by sacrificing the soldiers of the military.

King Bradley arrives at the military base, and has a private conversation with Kimblee, where he is given the instructions to go into Lior and cause trouble, and return with Ed's dead body. Marta overhears this and also discovers that King Bradley is actually Pride, the seventh and final homunculus, whose Ultimate Eye is hidden under the eyepatch. She encounters Al and hides inside him, but King Bradley comes and sticks his sword inside Al, tragically killing Marta.

Scar, speaking for Rose, tell the people of Lior to lure the military into the city, but not to provoke them. Kimblee, with a group of chimeras, attack civilians in the city, and Scar instructs the civilians to leave the city, so that he can create the Philosopher's Stone when the military arrives.

Ed sends a letter to Mustang explaining all that's happening in Lior, and advising him to keep the military from entering the city. Mustang and his group learn about what happened at Laboratory Five in Central, and how a Philosopher's Stone is made. Mustang tells Alphonse to go into Lior and find his brother. Frank Archer prepares to assault the city of Lior, but is ordered to wait by King Bradley. When Lust asks King Bradley (Pride) why he told Archer to wait, he said he was acting upon their master's orders. Angry, Lust decides to go into Lior alone so she can help Scar create the Philosopher's Stone.

Ed and Rose help the civilians exit the city of Lior, and Wrath and Sloth confront Ed. Wrath's weakness is revealed, and Wrath then attacks Rose, who manages to speak and call out to Ed to get his attention. Scar confronts Kimblee, and they begin an alchemic battle, causing more destruction in the city. Alphonse intercedes by trapping Kimblee, but he escapes and uses his alchemy to begin transforming Alphonse's armour into a bomb.

Alphonse's armour is slowly transforming into an explosive compound following Kimblee's attack. With Edward helping the Liorites escape, Scar is the only one who can help Alphonse. Scar then proceeds to turn Alphonse into the Philosopher's Stone. Seeing that Kimblee has been killed by Scar, Archer orders the military army into Lior to take him down. After multiple gunshot wounds, Scar takes his last breath and transmutes the whole city with the soldiers inside. Upon seeing the destruction, Ed races to find Scar. Finding his brother alive, Ed soon realizes what Scar has done. Lust then appears, instructing the brothers to start running; that they will soon be sought after.

A complete stranger tries to strike up a conversation with Winry upon the arrival of Winry and Sheska in Resembool. Pinako introduces him to Winry as Edward and Alphonse's father, Hohenheim of Light. Meanwhile, the Elric brothers flee Lior for Resembool, while Mustang's brigade, on orders from Bradley to capture the boys, is in hot pursuit. Once cornered, Mustang explains to the brothers that he is not after them due to military orders, but because he is angry at them for not seeking his protection.

Rose and Lyra descend a secret staircase in an old church. Later, Hohenheim decides to confront the leader of the homunculi.

As Hohenheim battles the leader of the homunculi, who is revealed to be Dante, their common history is revealed.

Tucker makes a quid pro quo with Alphonse, offering to show Alphonse how to use the philosopher’s stone in exchange for using the stone to resurrect his daughter Nina, while Lust offers to help Edward in exchange for making her human.

As Edward, Lust, Wrath, and Sloth all arrive at the factory where Alphonse went to meet Tucker, a climactic battle ensues, as Edward and Alphonse must finally confront their creation.

Entrenched at the northern border with Drachma, Armstrong declares his and Mustang's intention to rebel against the Führer. Meanwhile, as Alphonse, Edward, and Wrath see Sloth evaporate, Envy enters, disguised as Winry, and kidnaps Alphonse. Edward begins to chase after Envy but is stopped by Wrath, who begins attacking him. Izumi arrives, distracting Wrath, and he runs into the woods, and Izumi and Edward leave to confront the other homonculi.

The Tringham brothers have arrived in Central with an important message for the Elric brothers. However, while in a bookstore, Russell pretends to be Edward again to get out of paying for some books. Sadly, Russell and Fletcher find themselves captured, the military believing them to be the real Elric brothers. The Führer sentences them to death, but they are saved by Denny Brosh and Maria Ross. The four of them run into Edward and Izumi, who are trying to find the Führer. However, they are confronted by Frank Archer, who has turned into a cyborg being. Izumi stays to confront Archer, and she orders everyone else to leave.

Trying to find another way to reach the Führer, Edward stops a car and notices Mustang and Hawkeye inside, both of whom have been hiding in Central so they can attack the Führer without him expecting. Mustang has Edward enter the car and during the car ride Edward and Mustang finally have a chance to repair their friendship before they go their separate ways.

Envy delivers Alphonse to the leader of the homunculi in the city hidden beneath Central. Edward soon discovers the city thanks to a page from Nash's diary, leading to a final confrontation with Dante. Edward also learns that Dante is planning to transfer her soul to Rose's body using the philosopher's stone from within Alphonse. She then sends Edward through the Gate of Truth and he awakens to find himself and Hohenheim in a war-torn London.

As zeppelins rain bombs upon London during World War I, Edward and Hohenheim flee the city. As they watch the attack from a distance, Hohenheim explains that in this world, on the other side of the gate, the science of physics has developed instead of alchemy but, because Ed's soul was transferred over without his body, the Gate of Truth within himself can be used to return to Amestris. Meanwhile, with the help of Riza Hawkeye, Mustang has sneaked into Bradley's mansion to confront him and avenge Hughes's death. Edward returns to Amestris and tries to stop Dante's plans and set Alphonse and Rose free, only to be stabbed down by Envy in a short battle when he reveals himself as Hohenheim's son. However, Rose comes out of Dante's control and begins calling out for Edward.

Alphonse attempts human transmutation on Edward using himself as material for equivalent exchange. Edward reawakens to see that his arm and leg are now flesh and blood, however, Alphonse has been taken by the Gate of Truth as a consequence. Edward then attempts human transmutation, offering his own life, allowing Alphonse to return back to his body, albeit his memory is recalled up to when the brother tried to resurrect their mother. Meanwhile, Mustang successfully kills Führer Bradley with the help of Selim Bradley, who unintentionally weakens his adoptive father by bringing him the remains of the human from which the Führer was originally based. The Führer responsively kills his son out of anger before Mustang takes his advantage. Alphonse is back in Amestris now and Edward is pulled through the Gate of Truth and is currently in Munich. The brothers both resolve to meet each other again someday.

Edward Elric and Alphonse Elric, who both have already made a strong reputation of themselves despite Edward's short military career, are called upon by Fuhrer King Bradley and Colonel Roy Mustang to hunt down rogue state alchemist Isaac McDougal. Edward and Alphonse ambush and successfully capture their target. However, due to Edward's carelessness, the Freezing Alchemist finds an opening and escapes. The Elric brothers alongside the state military are forced to confront McDougal again when he simultaneously activates numerous transmutation circles in Central, which creates an alchemic reaction encompassing the entire command centre. Edward suspects the use of a philosopher's stone, but is unable to confirm his suspicion. Luckily, the Elric brothers, Major Alex Louis Armstrong, and Mustang succeed in thwarting McDougal's plans to bury Central in ice. The Fuhrer confronts McDougal as he attempts to escape. In the brief battle that follows, McDougal is easily cut down by the Fuhrer, who later credits both Mustang and the Elric brothers in helping accomplish the mission.

As Edward and Alphonse depart for Liore by train, their childhood is shown in flashback. They had learned rudimentary alchemy from their father's books, and, upon their mother's death, had attempted to revive her by performing human transmutation, a practice officially considered taboo among alchemists. A dark mass of shadowy hands then proceeded to disintegrate Alphonse's physical body, while a disembodied figure named Truth showed Edward the secret behind perfect human transmutation in exchange for his left leg. Cursing his actions in causing the loss of his brother, Edward bonds Alphonse's soul to a suit of armour, sacrificing his right arm to complete the process. Elsewhere in the present, Colonel Maes Hughes shows Mustang the paperwork concerning the McDougal incident, which states that McDougal used a Xingese art known as alkahestry, unknown to the two of them. Back in the past, Edward's skill in both surviving the attempted human transmutation and anchoring his brother's soul attracts the attention of Mustang, who suggests Edward become a state alchemist. Edward later takes and passes the state alchemist examination, and is given the title of Fullmetal Alchemist.

Edward and Alphonse arrive at Liore, where they witness Father Cornello winning the devotion of the townspeople by performing miraculous transmutations, which they believe could only have been accomplished using a philosopher's stone. They meet Rose and request to see Cornello, who is aware of the state alchemists' presence. Cornello ambushes Edward and Alphonse, sending a chimera, a human-animal hybrid, after them. While battling the chimera, Edward unintentionally reveals his prosthetic automail limbs, making Cornello realize that he had attempted the forbidden taboo of human transmutation. Edward and Alphonse escape, taking Rose with them. While Alphonse explains their story to Rose, Cornello finds Edward and reveals his nefarious plan, unaware that it had been broadcast to the whole town of Liore. Cornello uses the philosopher's stone on his ring to fight against Edward, but Edward manages to defeat him. Edward then realizes that the stone is a fake when it shatters on the ground. Cornello runs off, but is killed by Lust and eaten by Gluttony. When Rose confronts Edward and Alphonse about the stone, despairing that she had believed in Cornello for nothing, Edward tells her to find strength within herself and to walk on her own two feet.

A mysterious man with a cross-shaped scar across his face attacks and murders Brigadier General Basque Grand. The Fuhrer orders Hughes and Armstrong to use all available resources to stop the murderer. Meanwhile, to avoid being in their debt, Mustang introduces Edward and Alphonse to Shou Tucker, the Sewing-Life Alchemist, who obtained his state alchemist credentials by creating a chimera that could understand human speech. He opens up his library to the Elric brothers for them to study living creature transmutation, but they also end up spending time to play with Tucker's daughter Nina and family dog Alexander. Upon returning to the house for another study session, they find that Tucker has created another speaking chimera in order to satisfy his yearly assessment requirements. However, Edward is furious to discover that the speaking chimera was created using Nina and Alexander, and he also realizes that Tucker did the same with his wife, two years prior. Alphonse stops Edward from nearly beating Tucker to death, as Edward is left feeling helpless. Mustang tells him that by being a state alchemist, he must prepare himself to take a life if called upon by the military. While Tucker is under arrest for his actions, he is visited by the scarred man, who kills him and the chimera.

Lieutenant Riza Hawkeye tells Edward and Alphonse that both Tucker and the chimera have been killed. Meanwhile, back in Liore, Lust and Gluttony attempt to cause a rebellion using the faith of the locals, with Envy using his shape-shifting powers to disguise himself as Cornello. Back at East City, as Edward and Alphonse dwell on their limits in alchemy, they are viciously attacked by Scar. They quickly retreat until they are cornered and are forced to defend themselves, resulting in Scar damaging Alphonse's body and then destroying Edward's right arm. The state alchemists intervene just when Scar prepares to finish off Edward. Mustang, unable to subdue Scar, is saved by Hawkeye, who reminds Mustang that his flame alchemy is useless in the rain. When Armstrong arrives and battles Scar, it is revealed that the man is an Ishvalan. Outnumbered, Scar manages to escape into the sewers, and Mustang tells the Elric brothers about the Ishval civil war. Edward and Alphonse then decide to head back to Resembool to repair their bodies.

While Armstrong escorts Edward and Alphonse back to Resembool by train, he spots a man named Tim Marcoh, the Crystal Alchemist, at a nearby stop. He explains that Marcoh was a state alchemist and doctor during the Ishval civil war, and conducted research on biological alchemy before disappearing at the end of the war. They decide to chase after Marcoh, only to learn that he was researching the philosopher's stone. He had succeeded in its creation, though it is still incomplete. At first refusing to share his knowledge with Edward, Marcoh eventually gives them a clue to the location of his research data. After they reach Resembool, Winry Rockbell and her grandmother Pinako Rockbell start working on Edward's automail. After receiving his replacement arm and leg, Edward uses his alchemy to rebuild Alphonse's suit of armour from the shattered remains. Afterwards, the Elric brothers, along with Armstrong, head back to Central to search for Marcoh's research.

Edward and Alphonse arrive back in Central, only to find that the first branch of the state library had been burned to the ground. Scar encounters and battles Lust and Gluttony in the sewers, resulting in a large explosion. Edward and Alphonse's new escorts, Denny Brosh and Maria Ross, direct them to Sheska, a file clerk who had worked at the first branch of the state library, but was fired for spending all her time reading. Sheska reveals that she has memorized all of Marcoh's works, and then makes handwritten duplicates for the Elric brothers. While initially appearing to be a cookbook, Edward notices that is written in a code that Marcoh created. Edward and Alphonse spend several days deciphering the hidden data, only to discover that the philosopher's stone is made from living humans. Edward asks Brosh and Ross to keep it a secret, but Armstrong learns about it using intimidation. Edward notices another hidden piece of information, locating an unused laboratory next to a prison, where raw materials for the stone were gathered. Armstrong tells the Elric brothers to stay put, but they both manage to sneak out to the fifth laboratory. Edward enters the building via an air duct, while Alphonse waits outside, unaware that he is being watched by a menacing figure.

At the fifth laboratory, Al fights Barry the Chopper outside, and Edward faces Slicer inside. It is revealed that both opponents are souls of murderers affixed to armour. Edward struggles in his battle when his automail arm malfunctions, the result of Winry forgetting to add a small bolt back in Resembool. Alphonse initially has the advantage in his fight, until Barry suggests that Alphonse never truly existed, saying he was a doll made for Edward. Contemplating on the possibility, Alphonse recalls that Edward was afraid of telling him something. Edward is particularly troubled when his opponent turns out to be a pair of brothers, each controlling a different part of the armour. Edward manages to defeat Slicer by use of Scar's destruction technique, but before he can get any information from the two brothers, they are killed by Lust and Envy. Edward demands to know who they are and tries to use alchemy, but his automail arm breaks and he gets knocked out by Envy. Outside, Barry almost gets the upper hand on Alphonse, but he is saved by the arrival of Brosh and Ross. Lust and Envy destroy the lab to cover up the evidence of the philosopher's stone, but not before carrying Edward outside and handing him over to Brosh and Ross, commenting that he is a valuable resource.

Edward and Alphonse are hospitalized following the incident of the fifth laboratory. Ross slaps Edward for being reckless, and asks him to trust adults more. Needing his automail repaired, Edward calls for Winry to come to Central. When Winry arrives at the train station, Alphonse still contemplates what Barry had told him. Hughes invites Winry over to his daughter Elicia's birthday party, where she laments that Edward and Alphonse never tell her anything. Hughes tells her that men tend to hide things so as not to worry anyone. Alphonse then decides to confront Edward about what he was afraid to tell him, asking if he was really an artificial soul. Edward storms off and Winry yells at Alphonse, telling him that Edward was terrified that Alphonse blamed him for getting him stuck in the armour. The Elric brothers then have a fight, which Edward becomes the victor, and they both reminisce about their past fights, reaffirming their existence. Meanwhile, Scar wakes up in the care of Ishvalan refugees.

Bradley appears at the hospital and warns the Elric brothers to be careful around the military, and he then hops out of a window to evade his subordinates. Edward and Alphonse decide to go to the town of Dublith to visit their alchemy teacher, Izumi Curtis, to ask her for information about the philosopher's stone. They agree to take Winry with them when she notices that Rush Valley, a town best known for its automail shops, is on the way to Dublith. Hughes investigates the problems in Liore, the fifth laboratory, and the Ishval civil war. He discovers a connection, but is then attacked by Lust. He escapes her and tries to contact Mustang with his information at a public telephone booth, only to be gunned down by Envy disguised as Ross, and then as his wife Gracia. Hughes is posthumously promoted to the rank of a brigadier general. Mustang investigates the murder of Hughes, and concludes via Armstrong that a high ranked member of the military may be responsible for the command of Hughes's death.

As Edward, Alphonse, and Winry arrive in Rush Valley, Edward's state alchemist pocket watch is stolen by a pickpocket named Paninya, who has automail legs. After tracking her down, Winry asks her automail's creator, Dominic LeCoulte, to let her be his apprentice, but is swiftly declined. As Winry convinces Paninya to stop being a pickpocket and return the pocket watch, she peeks in it and finds the date the Elric brothers burned down their house carved inside. Meanwhile, one of the residents is having a baby, and since they are unable to travel to a hospital in the poor weather, Winry decides to deliver the baby. Following a successful birth, Winry asks again to be an apprentice, and Dominic directs her to another mechanic where she can study to become a better automail engineer. With that, Edward and Alphonse continue onwards to Dublith.

Edward and Alphonse visit Izumi and her husband Sig in order to get clues on the philosopher's stone. During their stay, the Elric brothers recall how they first met Izumi during a flooding in Resembool, and how they had been formally accepted as Izumi's disciples after being stranded on an island for a month. They look back at how they figured out the meaning behind one is all, all is one. Izumi notices that the Elric brothers attempted human transmutation, concluding this from their movement during hand-to-hand combat training. Realizing that they were not the only ones who had committed the taboo, Izumi tells the Elrics that she also had attempted human transmutation to bring back her child, who died when Izumi became sick during pregnancy. The three make up, bonding over the hardships that they went through after suffering the effects of human transmutation.

Edward and Alphonse are no longer pupils of Izumi, rather they are her equals. Meanwhile, Mustang announces to his five subordinates that they are all transferring back with him to Central. Scar, recovering in an Ishvalan squatter colony, is advised by the elder that pursuing the current state alchemists would not do the surviving Ishvalans any good. Scar leaves the colony after having to defeat two thugs recruited by Yoki, who wanted to capture Scar and bring him back to Central, due to his connections to the murder of Basque Grand. Alphonse, lured to a trap after reading a threatening note regarding his secret, is captured by Roa, Bido, Martel, and Dolcetto, all of whom are chimera under the homunculus Greed. Edward finds Greed, who proposes teaching homunculus fabrication in exchange for learning human transmutation. An enraged Edward charges at Greed, who uses his ultimate shield to make himself invulnerable to Edward's attacks. However, Edward is soon able to counterattack by transmuting Greed's ultimate shield. Izumi arrives and intervenes, taking Greed by surprise.

Bradley and Armstrong lead a team of state military soldiers to raid Greed's hideout, though the former is using it as cover to hunt down and execute Greed. The state military soldier’s fire at Roa and Dolcetto, but the two survive. Bradley goes into the sewage passageway beneath the hideout, and he duels against Greed there. However, Greed is severely weakened by the Fuhrer, who reveals his true identity as Wrath. Roa and Dolcetto, who have come to save Greed, are killed by the Fuhrer. Martel, who is hiding inside Alphonse, attempts to choke Bradley to death, but she is stabbed from outside the armour. Her blood splashes on Alphonse's blood seal and unlocks his forgotten memories. Alphonse reveals to Edward that he managed to recover all of his memories prior to being taken away from the Gate of Truth when Edward failed in his human transmutation attempt to revive their mother. Greed is taken back as a captive to Father, who was disappointed in him after he deserted the rest of the homunculi. When Greed refuses to re-join the homunculi, he is killed by being melted alive down to a liquid philosopher's stone, which is then consumed by Father.

Scar quickly deals with another state alchemist named Giolio Comanche, known as the Silver Alchemist. Upon returning back to the temporary hideout with Yoki, Scar discovers a young Xingese girl named May Chang accompanied by a tiny panda named Shao Mei, who have travelled across the eastern desert in search for the philosopher's stone. Meanwhile, Barry the Chopper is detained by Roy Mustang, Riza Hawkeye, and Vato Falman to be interrogated regarding the assassination of Maes Hughes. Elsewhere, the Elric brothers return to Rush Valley to have Edward's automail repaired once again. They then find a Xingese man named Ling Yao on the verge of starving to death. After being fed, he explains his purpose for researching alkahestry. Lin summons his bodyguards, Lan Fan and Fu, and holds the Elric brothers hostage, in hopes of having the secrets of the philosopher's stone revealed. During their fight, much of the town becomes damaged. Ling and his bodyguards retreat after their defeat, forcing the Elric brothers to confront the angry townspeople. Ling meets with Edward and Alphonse again after they repair the town, and it is realized that Ling wants to become the heir to the throne by learning about the philosopher's stone. Winry joins up with them, as they all prepare to depart for Central. Scar and Yoki are travelling to Central at night in a horse carriage with May in tow.

Edward, Alphonse, and Winry arrive in Central, though Ling gets arrested for being an illegal immigrant. Sheska accidentally reveals some information on Mustang to Envy, disguised as Captain Focker, one of her superiors. Armstrong informs Mustang that he was unable to tell the Elric brothers about Hughes's death. When they meet up with Mustang, he falsely says that Hughes has retired from the state military. However, they soon learn the truth after encountering Ross. Winry soon finds out the truth as well after visiting Gracia and Elicia. Edward, along with Alphonse, arrive to apologize, since Edward blames himself for Hughes's murder. Gracia encourages them to push forward, even though she is holding back her tears. Envy comes up with a plan to stop Mustang from investigating Hughes's death, and the next day Ross is arrested by Colonel Henry Douglas as a suspect for Hughes's murder.

Ross, accused of Hughes's assassination, is placed under military police custody and interrogated by Douglas. After reading a newspaper article about Ross's detention, Barry the Chopper leaves the safe house and launches a solo raid on the jail. Barry releases Ling from jail as well after Ling promises to help both Barry and Ross. Barry tells Ross that she needs to leave Central immediately, or risk being killed. Edward and Alphonse run into the trio, and Barry holds the brothers off to allow Ross time to get away. Ross then runs into Mustang, who seemingly kills her in a massive explosion. Edward accosts Mustang after seeing Ross's charred body, while Mustang coldly reminds Edward of his place as a soldier of the state military. Armstrong later shows up and declares that Edward should return back to Resembool to apparently have his automail arm fixed, dragging the confused Edward away.

Once they arrive in Resembool, Edward and Armstrong meet up with Heymans Breda, who takes them to the ruins of Xerxes. Once there, they discover that Ross is still alive, and that Mustang faked her death in order to draw out those responsible for Hughes's death. After the brief reunion, Ross decides to hide out in Xing with Fu, but promises to return if she is ever needed. After Ross's departure, Edward explores the ruins further and encounters a group of Ishbalan refugees, who reveal that it was Scar who had killed Winry's parents during the Ishbal civil war. Meanwhile, Barry's human body, which is now nothing more than a crazed animal, attacks Falman and Barry back in Central. However, with the assistance of Jean Havoc, they manage to subdue Barry's human body. Hawkeye, also there with them, is then attacked by Gluttony.

Kain Fuery manages to save Hawkeye, with Mustang coming to defeat Gluttony. Alphonse meets up with the group and they pursue Barry, who chases his body into the depths of the third laboratory. The group splits into two teams. Mustang and Havoc are ambushed by Lust, resulting in both men being grievously wounded and left for dead. Lust then confronts Barry, slicing him to pieces. Hawkeye, believing Mustang to be dead, flies into a suicidal rage and shoots Lust repeatedly, without effect. Before Lust can kill Hawkeye, Mustang appears, revealing he sealed his wounds by burning them shut. He repeatedly sets Lust on fire until her philosopher's stone is depleted. No longer able to regenerate, she crumbles to ash. Barry's soul survives, but his blood seal is scratched out by his human body, which kills both of them. Edward returns to Resembool and heads toward the Rockbell residence. However, he spots his father Van Hohenheim at the grave of his mother Trisha Elric.

An unhappy Edward overhears a conversation Hohenheim has with Pinako about whether or not the corpse that the Elric brothers had attempted to transmute was actually his mother. Hohenheim leaves the next day, warning Pinako that something horrible will happen in this country. Alphonse explains to Ling the circumstances of his body, and Winry is appalled when Ling doesn't care about the consequences of Alphonse's body. Determined to find the true answer, Edward and Pinako dig up the corpse of the failed transmutation during a downpour, though Edward keeps retching at the thought. When the body has been unearthed, he realizes it was not their mother that they transmuted. Edward then calls Izumi and asks about the legitimacy of her human transmutation, but she does not answer. Edward returns to Central and reunites with Alphonse and Winry, reassuring them of the possibility of restoring Alphonse's body. Izumi calls Edward back, saying she had the same results as him, which confirms his suspicions of the possibility, but not of reviving what has been deceased. Edward, Alphonse, and Izumi feel a sense of relief that they had not killed their loved ones a second time. The Elric brothers reaffirm their resolve to return Alphonse to his original body.

Edward ponders on the assumption that Alphonse may be absorbing some nutrients through him. Mustang suspects that the Fuhrer is cooperating with the homunculi. Havoc reveals the lower half of his body is paralyzed, and Mustang feels a bit of remorse for that. Scar has returned to Central and murders three more state alchemists. Edward and Alphonse dangerously plan to confront Scar in order to draw out the homunculi. Ling and Lan Fan appear and agree to help them, as it would benefit Ling in finding immortality. Mustang sends Breda to locate Marcoh, only to find he has been kidnapped. Edward begins showboating in the streets, eventually luring in Scar. While the Elric brothers fight him, Mustang goes to the command centre and reports false information regarding the whereabouts of Scar, confusing and stalling the state military. Lan Fan attacks Gluttony, but is soon injured by Bradley.

Ling fights Bradley and Gluttony as he tries to escape with Lan Fan. Meanwhile, Winry hears about the Elric brothers fighting Scar and heads over there. As she arrives, she hears Edward questioning Scar about the death of her parents. Shocked by this, Winry picks up a nearby gun and aims it at Scar. It is then that Scar recalls about his brother who had researched into alchemy to combat against the attacking state alchemists. However, they had been attacked by Solf J. Kimblee, the Crimson Alchemist. Scar had been heavily injured from the attack, as his right arm had been brutally severed. To save him, his brother had sacrificed himself and had transferred his right arm onto Scar. Shocked upon waking up and seeing his brother's arm on his body, he went berserk and had killed Winry's parents. Before they can kill each other, Edward protects Winry from Scar and interrupts Scar's attack in its tracks, reminding him of when his brother protected him. A concerned Edward consoles a traumatized Winry, while Alphonse chases after Scar. As he slowly has her unclasp the gun, he tells her that her hands were meant to give life and not to kill.

Edward leaves Winry in the custody of the state military in order to catch up with Alphonse. Meanwhile, as Bradley continues to chase after Ling and Lan Fan, Gluttony goes after Scar. As Edward re-joins Alphonse in his fight against Scar, Gluttony arrives on the scene. Ling then joins the fight and is able to capture Gluttony. Lan Fan manages to escape Wrath by cutting off her disabled arm and strapping it on the back of a dog to throw Wrath off her trail. Hawkeye arrives and drives off with Ling and Gluttony, keeping the operation secret from the state military. As the Elric brothers are about to apprehend Scar, they are stopped by May, who uses her alkahestry to escape with him. However, the Elric brothers manage to take custody of her panda, Shao Mei. As they arrive back at the headquarters, they tell Winry everything. Winry feels depressed, believing all she can do is wait, but feels better when she receives a call from her customers back in Rush Valley. As she leaves on the train back to Rush Valley, Winry starts to realize that she may be falling in love with Edward. Meanwhile, Edward and Alphonse join the others at a hideout, where Lan Fan's wounds are treated by Doctor Knox. Ling reveals to Edward, Alphonse, and Mustang that the Fuhrer is a homunculus. When Gluttony hears mention of Mustang, the one who killed Lust, he transforms and blows the corner off the hideout.

Marcoh, in the custody of the homunculi, has to cooperate in exchange for his village's safety. Meanwhile, Edward, Alphonse, and Ling try to escape from Gluttony, who has become able to swallow anything in his sight. After losing Gluttony, Dr. Knox takes Mustang, Hawkeye, and Lan Fan to safety while Edward, Alphonse, and Ling stay to fight. Envy arrives to stop Gluttony from harming the Elric brothers. Hearing this, Edward and Alphonse face Gluttony while Ling battles Envy. After some fighting, Gluttony ends up accidentally swallowing Edward, Ling, and Envy. Mustang stumbles upon a conspiracy between the Fuhrer and the top brass of the state military and realizes that this is what Hughes meant when he said the state military was in danger.

Edward and Ling find themselves in a dark place and realize they are inside Gluttony's stomach, as they try to find a way out. May is worried about Shao Mei, explaining to Yoki about their circumstances, so Scar decides to help search for her. Edward and Ling are approached by Envy, who explains that Gluttony was a failed attempt at recreating the Gate of Truth, and that there is no exit. Envy, after revealing that he was the one who started the Ishval civil war, transforms into a giant beast. Meanwhile, Alphonse gets Gluttony to take him to Father, who is apparently in Central, and Wrath gets leverage over Mustang by transferring his men to various military command headquarters and assigning Hawkeye as his personal assistant, effectively making her his hostage.

Edward and Ling face off against Envy. Edward, finding himself hesitating to attack, due to all the people embedded into Envy's body, gets swallowed. Meanwhile, Scar and May find Shao Mei with Alphonse and Gluttony and decide to follow them down to an underground tunnel, where they fight off several chimeras. Edward spots the philosopher's stone inside Envy, and, after seeing the missing piece from the ruins of Xerxes found in Gluttony's stomach, he conjures a way to escape. Bradley explains to Mustang how he was trained from birth for leadership and was injected with the philosopher's stone. Edward reluctantly uses the souls inside the stone to transmute himself and open the Gate of Truth to escape through. Edward finds Alphonse's body but is unable to bring it back, since it is not his. However, before the gate closes, he bursts through it, yelling to Alphonse's body that he will come back to get him someday.

During a festival in Resembool, Hohenheim converses with a young Pinako, who asks him why he remains apart from all the villagers. In the same time, he faces a demon identical to him who talks to him about the weakness of the humans, as the story so far is recounted. In the end, Hohenheim finds encouragement from a young Trisha, and he wakes up to discover it was all a dream as a result of drinking too much alcohol.

Alphonse and Gluttony arrive at Father's lair, when Edward, Ling, and Envy burst out of Gluttony's stomach. Father then uses his strange powers and cancels out Edward and Alphonse's alchemy, rendering them vulnerable. Ling is then captured and given the philosopher's stone, which he willingly accepts, allowing Greed to take over his body. Scar and May then arrive and engage in battle, where their alchemy is still effective. Scar learns about the murder that Envy committed which triggered the Ishbal civil war and attacks Father, only to find his powers ineffective against him. May gets injured, and Scar uses a hydrogen explosion as a diversion so that they can both escape. Edward battles Greed and is quickly subdued, although he can sense that Ling is still inside Greed. As a result of the earlier explosion, Gluttony uses up the last of his regenerative abilities, so Father extracts his philosopher's stone, promising to revive him with his memories intact.

Envy leads Edward and Alphonse, who has May and Shao Mei hidden inside of his armour, out of Father's hideout, which is actually under Central Command Headquarters, to meet with Wrath. Though Edward tries to resign from the state military, Wrath threatens to kill Winry unless he remains a state alchemist. However, he allows the Elric brothers to continue their research. Bradley denies having killed Hughes when asked by Mustang, but refuses to reveal the killer's identity. Edward calls Winry to assure her safety. Greed gives Alphonse a message written by Ling, in order to notify Lan Fan that he has found the philosopher's stone. Meanwhile, Scar encounters an imprisoned Marcoh, who admits being responsible for the extermination of the Ishbalans. Meeting up with Bradley, Greed points out that Ling is still fighting for control of his body. Mustang reveals Bradley's true identity to Armstrong, as he ponders that there may be another homunculus lurking in the shadows. Alphonse, taking May to be treated by Knox, informs Lan Fan about Greed, encouraging her to get an automail arm. Edward, hearing that other alchemists had failed to transmute at the same time his abilities were blocked by Father, wonders how Scar and May were still able to use theirs. Even though Marcoh begs for Scar to take his life, Scar demands to know how Marcoh was involved in the civil war.

Years ago, Mustang's desire to become a state alchemist was disapproved of by his teacher, Berthold Hawkeye, who was Riza Hawkeye's father. Before dying from an illness, he asked Mustang to look after his daughter, who has the details of his flame alchemy research tattooed on her back. In the present, Edward visits Hawkeye and returns the gun she lent him, explaining his inability to pull the trigger. After the civil war had broken out seven years past, Bradley signed a document announcing the extermination of the Ishvalans. It took a toll on many state alchemists, including Hughes and Mustang, which was not helped by the taunts of the hardhearted Kimblee. Marcoh reveals to Scar that he was involved in using Ishvalans to make the philosopher's stone, which was given to the state alchemists to enhance their alchemy. The Ishvalan leader tried pleading with Bradley to end the killing in exchange for his life, but he was rejected. When the civil war finally ended, Mustang resolved that he would work to become the new Fuhrer to protect the people, and appointed Hawkeye as his second-in-command. Hawkeye mentions to Edward that when they finally achieve peace, they may have to be punished for the crimes they committed during the war. When Envy checks Marcoh's prison cell, he finds a beheaded corpse and the word vengeance written in blood on the wall.

After contemplating as to why Scar and May could transmute when the alchemy has been blocked at the time, Edward and Alphonse go and look for May and Shao Mei. Meanwhile, Mustang's subordinates say their goodbyes as they are sent to different state military bases. Mustang later reminds Edward that he owes him five hundred and twenty cens, but Edward decides to keep the money until Mustang becomes Fuhrer. Mustang uses the note he got from Falman to make contact with Commanding Officer Grumman. Meanwhile, Fu is shocked to find Lan Fan had lost her arm, yet they decline to see an automail mechanic, since it would put Winry in danger. Afterwards, Knox gets a visit from his wife and son, who are pleased to hear he treated two live patients. Suspecting that Marcoh had escaped along with Scar, Envy releases Kimblee from prison and gives him the task of retrieving Marcoh and killing Scar. Wanting to find out more about Kimblee and the secrets behind his brother's alchemy, Scar destroys Marcoh's face so it will not be recognized, before heading off towards the North to recover his brother's notes.

As May heads off towards the North with one hooded person, Scar escapes with another to the West. Grumman, disguised as a woman, meets up with Mustang to discuss current matters. Upon hearing that Grumman saw May at the train station, Mustang asks Armstrong to pass the message onto Edward, who had decided to look in the library for information on alkahestry. Upon passing on the message, Armstrong also gives Edward a letter of introduction to pass on to his sister Major General Olivier Mira Armstrong at Briggs Fortress. Later on, Edward and Alphonse meet the Fuhrer's adopted son, Selim Bradley, and are invited to his house where they also meet the Fuhrer's wife, and are later joined by the Fuhrer himself. After the meeting, the Elric brothers head off towards the North. Meanwhile, Scar and his accomplice escape from the train heading towards the West, and Kimblee tries to predict Scar's next move.

After some investigation, Kimblee deduces that Scar is headed towards the North. He manages to catch up to the train Scar is hitching a ride on, only to find his hooded companion is actually Yoki and not Marcoh. Scar and Kimblee recognize each other from when they crossed paths in Ishval, and a fight ensues. Scar manages to impale Kimblee, but Kimblee manages to separate the train carriages and escape. Meanwhile, May continues towards the North with Marcoh, while Edward and Alphonse arrive upon the mountain path leading to Briggs Fortress. They soon find themselves attacked by one of the soldiers, Captain Buccaneer, before being surrounded by the guards. They are then confronted by Olivier. May and Marcoh manage to find research notes written by Scar's brother and begin to decipher them.

After learning about what type of automail is suited for such snowy weather, Olivier asks the Elric brothers about the purpose of their arrival. Deciding not to mention anything incriminating, they speak of their search for May, leading Olivier to be interested in alkahestry. They are given work to do by Major Miles, who is part Ishvalan, and they also run into Falman. Suddenly, the homunculus named Sloth appears from underground, and Olivier is surprised by his invulnerability. Edward has to hold back his answers about the homunculus, only mentioning that its makeup is similar to that of a human, which gives Olivier an idea on how to detain it.

Olivier and her crew manage to subdue Sloth by dousing him in fuel and sending him outside to freeze. Olivier then has the Elric brothers arrested so she can learn more about the homunculus. Kimblee, who is in the hospital, is visited by Lieutenant General Raven, who brings along another state alchemist who uses the philosopher's stone to heal his wounds. Meanwhile, Marcoh continues to look into alkahestry, with May teaching him about how it works. Edward, Alphonse, Olivier, Buccaneer, and Falman investigate the tunnel that Sloth made, where Olivier has Edward tell her everything. Edward and Falman deduce that the tunnel is being used as a giant transmutation circle for the philosopher's stone, and that Amestris itself was formed for that very purpose. Olivier talks with Raven while the others listen in on the conversation, and gets him to spill about immortal armies.

Hohenheim recalls when he had left his family, lamenting that his body would outlast that of his wife and sons. Meanwhile, soldiers investigating the tunnels under Briggs Fortress find themselves under attack by a mysterious shadow. Raven tells Olivier to put Sloth back into the tunnel and seal it off. While Miles stalls Kimblee for time, Olivier kills Raven. As Olivier shows a few of her men a separate entrance to the tunnel, Kimblee brings Winry over to see Edward and Alphonse, reminding them of their place and situation. Meanwhile, Scar and Yoki reunites with May and Marcoh, and Mustang gets information and a message from Olivier from his intelligence sources.

Edward has his automail fixed by Winry, while Kimblee issues orders to keep Alphonse separated from Edward. Olivier sends a search party down into the tunnels, who find a couple of survivors that warn them not to put any lights on, or else a monster would come. Hawkeye learns that Selim is a homunculus named Pride, who attacks from the shadows. Kimblee orders Edward to search for Scar and Marcoh, and to create a blood crest similar to Ishval in Briggs Fortress, tempting him with a philosopher's stone if he accepts. After telling Alphonse and Winry about the situation, Edward grudgingly accepts the job, though he does not intend to use the stone himself. As the Elric brothers go to search for Scar, their real intent to find May as well, Winry decides to accompany them.

Hawkeye receives a call from Mustang, but is unable to say anything in fear of being watched by Pride. In the town of Baschool, the Elric brothers, along with Winry, lose the guards that were assigned to them, and end up running into May, Marcoh, and Yoki. It is explained how Yoki was banished from the state military. Elsewhere, Scar encounters a pair of chimeras under Kimblee named Jerso and Zampano, running into trouble with them. Scar gets pinned, but Edward and Alphonse arrive and beat the chimeras, before restraining Scar themselves. Winry and Miles arrive, and Winry confronts Scar face-to-face about the deaths of her parents. Explosions then are set off, and it appears that Scar has taken Winry hostage. Meanwhile, as Olivier's squad retrieve the survivors from the tunnels, Briggs Fortress is approached by Central Command Headquarters.

When faced with the option of judging the one who killed her parents, Winry decides to bandage Scar's wounds, knowing it would be something her parents would do. Miles explains to Scar that he joined the military to gradually change the way people think of Ishvalans. Since May and Marcoh need Scar to decipher his brother's research, Miles offers to hide everyone at the fort, with Alphonse insisting on sparing the two chimeras. While Scar and company head for the fort via tunnels in the mines, Winry comes up with a ruse to make it look like Scar has kidnapped her to elude Kimblee, just before a blizzard sets in. However, as they head for the fort, Miles gets word that Olivier is no longer there, as it is being manned by the state alchemists. When Alphonse willingly goes into the blizzard to find and warn the group, he briefly sees his body and wonders if it is trying to get its soul back. Meanwhile, Father makes plans involving Alphonse, Edward, Hohenheim, Izumi, and one more candidate.

Olivier goes to Central, where she admits to killing Raven and convinces Bradley to let her take his place. Hawkeye uses a coded message to tell Roy Mustang that Selim is a homunculus. Meanwhile, Father dreams of ancient Xerxes, where Hohenheim had been raised as a nameless slave, known only as Number 23. There, Hohenheim had met Homunculus, a being in a flask who was created from his blood, which gave Hohenheim his current name and taught him the basics of alchemy. One night, Homunculus had been summoned by the King of Xerxes, who asked Homunculus to tell him the secret for immortality. Homunculus had tricked the king into making a gigantic transmutation circle, using the whole country as a sacrifice, while it and Hohenheim stood at the centre of the circle. When Hohenheim had awakened, everyone else in Xerxes was dead, except for Homunculus. It had created a body shaped like Hohenheim for itself, then becoming known as Father. Back in the present, after Hohenheim awakes from this shared dream, he runs into Izumi and Sig. When Hohenheim notices that Izumi committed the ultimate sin, he rearranges her organs so that her blood can flow better. After this, Hohenheim tells Izumi and Sig that he is the philosopher's stone in human form.

Miles and his men set off with the intent of killing Kimblee and his henchmen, something Edward objects to. As Scar and company exit the mine, they find Alphonse, who warns them about Central Command Headquarters infiltrating Briggs Fortress, so Scar decides to take them towards an Ishvalan slum. Miles attempts to snipe Kimblee, but Kimblee has already figured out the trap and uses a cover of snow to enter the mines. Edward tries to follow, but is attacked by two more chimeras, Darius and Heinkel. Edward disables them by using the ammonia in dynamite to make a stink bomb to overwhelm their high sense of smell. Edward then knocks the philosopher's stone out of Kimblee's hand, but Kimblee uses another philosopher's stone hidden inside his mouth, sending Edward and the chimeras down a mine shaft and leaving Edward impaled by a steel bar. At the same time, Alphonse starts to drift out of consciousness, saying his soul is being drawn back to his body. Determined not to die, Edward gets the chimeras to remove the bar while he sacrifices some of his life span to temporarily fix the wound and to stop the bleeding. The chimeras find the philosopher's stone that Kimblee dropped, and, thankful for their rescue, decide to take Edward to a doctor.

Alphonse, after regaining consciousness, realizes he was dismantled by the group to carry him back to the tunnels. May figures how to decipher the notes written by Scar's brother by rearranging and overlapping the pages, which reveal the nationwide Amestris transmutation circle. After further investigation, they flip over the pages, finding another transmutation circle used for alkahestry. Meanwhile, Kimblee encounters Pride, who tells Kimblee to carve out the Briggs Fortress blood crest. Elsewhere, Falman gets into contact with Breda, and Sloth finishes digging the tunnels. Hohenheim arrives in Liore, where Rose and the other citizens are rebuilding, and finds an underground passage under the church of Leto. As he stumbles upon Sloth's tunnels, he is attacked by Pride but manages to escape outside its boundary, and then tells Pride to let Father know he would be coming. Meanwhile, in order to carve out the blood crest, Kimblee conspires with the Drachman military forces to attack Briggs Fortress, and Zampano informs Envy of Marcoh's location.

Briggs Fortress is able to defeat the Drachman military forces with ease, finally carving out the blood crest. Zampano brings Envy to Marcoh, where Marcoh reveals that it was their intention from the start to lure the homunculus out there, and Envy is easily hit and outsmarted by the multiple alkahestry traps set up by May. Out of anger, Envy transforms into his true form and begins to attack the group. After being captured by the homunculus, Marcoh destroys the philosopher's stone inside Envy, reducing him to his real form, a tiny, parasitic creature. Scar gives it to May and tells her to return to her country. Marcoh and Scar decide to go their own way, and Alphonse and the rest head for Liore. In Dublith, Bido, the last remaining chimera under Greed, sees two military officers searching for Izumi. Thinking that they could lead him to Greed, he hides underneath their car. Olivier is told about the fort's victory, and is then shown, by one of the superiors, the secret behind forbidding human transmutation. Meanwhile, when reaching Liore, Alphonse's group meets with Rose as well as Hohenheim.

Alphonse and Winry are welcomed by Rose and the people of Liore. Meanwhile, Darius, one of the chimeras who helped Edward after he had been injured, goes to a bank and makes a withdrawal from Edward's state alchemist research account. However, the state military is informed and they storm the clinic where Edward and the chimeras are, though the trio manages to escape from them. Hohenheim tells Alphonse the truth about himself and his involvement with Father. While Olivier is shown the army of artificial humans created by the military, Bido is spotted by Greed. Bido realizes who Greed is and tries to make him remember his chimera friends, but Greed ends up killing him. Angered at seeing Greed kill one of his friends, Ling's conscience has a vicious clash with Greed's. Later that night, Greed storms Bradley's mansion and confronts him.

Greed is initially overwhelmed in his fight against Bradley, but he manages to survive and escape. Meanwhile, Olivier requests, mainly as a means to avoid the family being taken hostage, that her father determine leadership of the household, which leads to a fight she inevitably wins against her brother. May passes through Youswell, and the people there offer to help her on her journey back to Xing, but Envy tricks her into heading back to Central. Edward, Darius, and Heinkel arrive at one of the old hideouts in Central and are soon met by Ling, who had managed to temporarily regain control over his body. Before Greed takes over again, Ling tells Edward that Father will try to open the gate on the Promised Day. Since Greed had severed his relationships with the homunculi, Edward suggests that Greed become his ally. Greed jokes that he just might consider it if they work for him, but Edward decides to take that suggestion seriously, and Greed accepts the offer. Alphonse passes a message to all military command headquarters, warning everyone about the Promised Day, which is set to take place next spring.

Briggs Fortress soldiers escort Winry back home, where she is surprised to find Edward and his group. Though Edward warns her to escape to another country, she refuses and says that Edward should just make sure he protects everyone. Meanwhile, Scar has recruited several Ishvalans to help in his cause, and Mustang informs about Selim's true identity to Olivier. Alphonse, who had been suffering from more frequent blackouts, is ambushed and captured by Gluttony and Pride. On the day before the Promised Day, Wrath is tricked into taking a train back to Central and is caught in an explosion on the bridge. Meanwhile, Hawkeye, Breda, and Fuery prepare for the upcoming day. Within the military, as the chosen generals are panicking over the Fuhrer's possible death, Olivier sees her chance to try to take control. However, before she can do anything, she is halted by the sudden appearance of Father and Sloth.

Upon seeing Hohenheim, Edward's group is notified about the Promised Day, and in return Edward tells of the last dying words Trisha had told him. Soon after, Edward's group leave, only to run into Alphonse. However, it is revealed that Alphonse is being controlled by Pride. Although it seems that Pride gets the upper hand, Edward responds by blacking out the slums and taking away the light so that Pride cannot use his shadows. Heinkel uses this opportunity to find and attack Pride, but Gluttony then fights Edward, Greed, and Darius. Greed, having a disadvantage in the dark, agrees to switch places with Ling, who uses his detection abilities to fight Gluttony. As Gluttony starts to use his full power, he is overwhelmed by the arrival of Lan Fan, who is now equipped with automail.

Ling and Lan Fan fight Gluttony, while Heinkel continues to fight Pride. Meanwhile, Mustang visits Madame Christmas to confirm that Selim is in fact a homunculus. Pride manages to overwhelm Heinkel. However, before Pride can finish him off, Edward intervenes and saves Heinkel using his automail, now reinforced with carbon. Spies from Central are shown to have followed Mustang to a hostess bar, finding out that Madame Christmas is his foster mother. Mustang then detonates the bar, and he escapes through the sewers with Madame Christmas. He then meets up with Hawkeye, Breda, and Fuery before they attempt to take over Central. Before Pride, who takes over Alphonse again, prepares to fight Edward, Fu throws a flash bang into the air, overwhelming the shadows with light and breaking Pride's control of Alphonse. Darius then takes Alphonse away to a safer place, and Gluttony stumbles into the fight between Edward and Pride. Upon discovering that Ling and Lan Fan can sense homunculi, Pride consumes Gluttony, both to replenish his live as well as to gain a sense of smell that can detect Edward's group. Back in Central, Mustang begins his upheaval plot by capturing Bradley's wife.

Edward, Greed, and Lan Fan have a difficult time fighting against Pride, since after devouring Gluttony. Alphonse intentionally allows himself to be captured by Pride, though instead grab onto him. Hohenheim encases the two in a mountain of soil void of light, thereby preventing Pride from using his shadows. Meanwhile, Kimblee begins to move just as Scar's group is told about the bombing of Bradley's train. As the Promised Day begins, Greed goes to Central on his own while both Edward and Scar's groups meet up again to devise a plan. In Central, Mustang and his subordinates begin to attack soldiers while using Bradley's wife as a hostage. However, the military superiors give the order to kill everybody in the group except for Mustang.

As Mustang's team are cornered by the Central soldiers, Mustang's old Ishval squadron intervenes and saves them. Meanwhile, the Briggs Fortress soldiers, led by Buccaneer, join the battle. As Mustang's team begins to run low on ammunition, they are saved by Maria Ross and Rebecca Catalina. Mustang calls the person who had Ross return from Xing, and he is surprised to hear Havoc at the other end. During the chaos, Edward's group manages to sneak underground via the third laboratory, where the group then splits up. Edward, Scar, Darius, Jerso, and Zampano go in one direction while Hohenheim and Lan Fan go in the other. However, at that moment, one of the generals awakens the mannequin soldiers.

As Edward's group arrives at the door where Alphonse had fought against Lust, the mannequin soldiers emerge from it. Meanwhile, Olivier is attacked by Sloth, who had been ordered to kill her. Alphonse and Heinkel learn too late that Pride had been sending a Morse code message from banging a stick onto Alphonse's head, and they are soon attacked by Kimblee, who frees Pride from his imprisonment. In the sewers, May is also attacked by the mannequin soldiers, and when Envy manages to merge with them, he returns to his regular form. As Olivier struggles against Sloth, Armstrong rescues her and joins the fight. Alphonse transmutes his legs off in order to help Heinkel, who then gives him the philosopher's stone that Kimblee had previously lost. Alphonse uses it to restore his legs, and then he faces against Pride and Kimblee.

Alphonse begins using the philosopher's stone to battle against Pride and Kimblee. He manages to trap Pride once again, but is taken by surprise by Kimblee when he starts using his own stone. Meanwhile, as the Armstrong siblings start to gain the upper hand over Sloth, it is then that Sloth begins to use his true strength and reveals himself to be the fastest homunculus. Although Alphonse gets apprehended by Pride again, Heinkel, having been healed by Marcoh, manages to deliver a fatal blow to Kimblee. Yoki arrives to rescue Alphonse and the others and head towards Central, while Pride consumes Kimblee. As Armstrong manages to temporarily impale Sloth on a spike, both he and Olivier are attacked by mannequin soldiers. Meanwhile, May fends off both Envy and the mannequin soldiers, while Edward's group, overwhelmed by the mannequin soldiers, are joined by Mustang and Hawkeye.

Mustang's team has Bradley's wife interviewed on a live radio broadcast. With the power of the broadcast and the help of the Ishvalans, word of a supposed coup d'etat spreads. This gives the rebels support from the citizens, while Briggs Fortress launches an attack on Central Command Headquarters. Meanwhile, Mustang manages to destroy the mannequin soldiers surrounding Edward's group by burning them to ash. May lures Envy into a trap in the upper levels, causing them both to fall below into the chamber with Edward's group. Envy reveals that he was the one who killed Hughes, infuriating Mustang who seeks to get revenge. Edward's group moves onward as Mustang fights Envy, but Edward gets concerned that Mustang may end up being consumed by his own hatred. Envy is no match for Mustang and flees for his life. Upon seeing Hawkeye heading towards Mustang for backup, Envy gets an idea. Mustang later encounters Hawkeye, who aims a gun at his back.

Upon seeing through Envy being disguised as Mustang, Hawkeye shoots Envy until the real Mustang arrives and mercilessly incinerates the homunculus, reverting him back to his parasitic form. Before Mustang can kill Envy, it is then that Edward, Hawkeye, and Scar persuade him to let go of his anger and his need for revenge, for Amestris cannot be ruled by someone consumed with hatred. Envy becomes outraged by Mustang's change of heart and rants about why everyone does not kill each other, trying to goad them into doing so by pointing out all of the terrible things they have done to each other. Edward determines that the reason why Envy hates humans is because he is jealous of their capacity to continue living on, despite all the abuse they take. Humiliated and insulted by how Edward understands him, Envy commits suicide by tearing out and destroying his own philosopher's stone. Meanwhile, the Armstrong siblings begin to gain the upper hand in their battle against Sloth. Izumi arrives in Central, allied with the Briggs Fortress soldiers, to participate in the coup d'etat. Elsewhere, Hohenheim confronts Father alone.

The Armstrong siblings have trouble fighting off both Sloth and the mannequin soldiers, until Izumi and Sig arrive. Through the combined efforts of Armstrong and Sig, they manage to deal enough damage to Sloth to finally kill him, before turning their attention to the mannequin soldiers. Meanwhile, Hohenheim fights with Father underground. In the midst of the battle, Father is unable to take the philosopher's stone from within Hohenheim, since the latter feels that he is missing something. With the majority of the Central Command Headquarters captured, the Briggs Fortress soldiers start to celebrate until Bradley, still alive, approaches the headquarters, promising to reclaim it.

Hohenheim, who had managed to converse with all the souls within his philosopher's stone, had infused the souls into Father's body to destroy it from the inside. However, Father shows his true form and is able to survive outside of his container, yet somehow he escapes from the inevitable and gets rid of his skin which appears to be a container. Meanwhile, Bradley begins his attack on the headquarters and solely takes on the resisting forces, as well as destroying Buccaneer's automail arm. As he reaches the main gate, he finds himself against Greed, and Bradley reveals his hidden ultimate eye to fight him. Buccaneer allows himself to be stabbed in order to take away Bradley's sword, though Bradley soon arms himself with daggers. Meanwhile, Falman and the remaining Briggs Fortress soldiers try to fend off the Central soldiers, and Fu later arrives to assist Greed in facing Wrath.

Greed, unable to hurt Wrath, is pinned down during their fight, which forces Fu to fight Bradley alone. Fu attempts to perform a suicide attack to kill Wrath using explosives strapped to his chest, but Bradley defuses them and mortally wounds Fu. However, Buccaneer thrusts a sword through Fu's body before he falls and successfully stabs Bradley in the stomach, allowing Ling to scratch out his ultimate eye, while Lan Fan arrives to witness her grandfather's death. Meanwhile, Edward's group encounters the gold-toothed doctor who created Bradley, and are pit against the numerous rejected Fuhrer candidates. The doctor then activates a transmutation circle, connected by the five research labs in Central, which absorbs Edward, Alphonse, and Izumi.

In the ensuing battle, Bradley ends falling into the moat below over the side of the front gate. As Buccaneer lays dying, he gives his final request to Ling to defend the front gate. Already distraught by Fu's death, Ling complies and draws upon the full power of Greed's ultimate shield to annihilate all Central forces before the gate. Underground, Edward and Izumi, with an unconscious Alphonse, reappear in Father's lair to find Hohenheim subdued. With four of the five human sacrifices, Father is left to wait for the fifth. The gold-toothed doctor in the levels above, has Hawkeye's throat slit, telling Mustang that he will only save her if he performs human transmutation as the fifth candidate.

Following Hawkeye's eye signal, Mustang refuses to perform a human transmutation. May arrives with Jerso, Zampano, and Darius and heals Hawkeye's wound. However, Wrath and Pride also appear and force Mustang to perform human transmutation, using the gold-toothed doctor as a sacrifice. Mustang passes through the Gate of Truth and reappears in Father's lair with Pride, Father, and the other sacrifices, and finds he has lost his eyesight in exchange. Scar battles Wrath above, and May crashes through the ceiling of Father's lair to find Alphonse unconscious. Alphonse stands before the gate to find his body, but despairs that he will be unable to use it to fight alongside the others because of its frailty. He promises to return for his body and goes through the gate, regaining consciousness in Father's lair and completing Father's count for the five sacrifices.

Edward and Alphonse battle against Pride, as May tries to take on Father by herself, all while the Ishvalans lay out alkahestry transmutation circles throughout Amestris. In his fight against Wrath, Scar reveals a reconstruction transmutation circle from his brother's research now tattooed on his other arm. Just as Edward's group starts to gain the upper hand, and despite the arrival of Greed, Father grabs the four sacrifices and uses them along with Hohenheim for his transmutation circle, absorbing all the souls in Amestris. This gives Father enough power to open the earth, allowing him to unlock the heaven in the sky and absorb the being within, referred to as the Eye of God.

Those who were present in the lair manage to survive the human transmutation, discovering how Father used over fifty million Amestrian souls only to suppress the Eye of God within a reborn body. Father neutralizes the use of alchemy, as he prepares to annihilate them. However, Hohenheim reveals his countermeasure, for having spent years traveling the country, placing fragments of his own philosopher's stone into the earth to use as foundation for returning the Amestrian souls to their original bodies. The stone fragments are activated by the eclipse's umbra, as the souls are ripped from Father's body back into their bodies, which forces a weakened Father to relinquish the Eye of God. As the eclipse then lifts, Bradley becomes blinded with sunlight, allowing Scar to kill him. Scar activates the nationwide alkahestry circle that his brother and fellow Ishvalans had been preparing, which restores the use of alchemy at the greatest potential. Unable to fight in his unstable body, Father retreats above ground to find more souls and replenish his stone supply. Edward remains behind to fight Pride while everyone else chases Father. Pride tries to steal Edward's body to replace his own deteriorating one, but Kimblee's soul reappears within him and taunts him while Edward enters his body and destroys it, reverting him to the form of a small fetus-like creature. Edward spares Pride's life and leaves to join his friends.

Hohenheim and the others stop Father from making more philosopher's stones, but as Edward re-joins them, Father spawns humans resembling the people of Xerxes before attacking with a powerful blast which takes out half the headquarters. They barely manage to survive the blast, but Alphonse and Hohenheim take some heavy damage protecting the others. Before Father can kill Edward and Izumi, the Briggs Fortress soldiers, along with several of Edward's allies, join up to attack Father and use up his stone supply. Father lets down his barrier temporarily to try to absorb Greed's stone, giving Edward, Armstrong, and Izumi the opportunity to damage him to the point of defending himself manually. As Father starts to lose control, he creates a blast which traps Edward's arm while his automail arm is destroyed. With Edward in danger, Alphonse convinces May to help him perform a transmutation, trading his soul for the return of Edward's right arm. Alphonse re-joins with his body on the other side and with his arm returned, Edward frees himself to unleash a series of blows on Father.

While being effortlessly pummelled, Father desperately tries to absorb the philosopher's stone from Greed. However, Greed who decides to part from Ling's body, and uses his carbonization ability to turn Father's body into weak charcoal. Father extinguishes Greed's soul, but Edward punches through Father's chest, releasing all the souls of the people of Xerxes and sending Father to the Gate of Truth where he is trapped for eternity. In the wake of Father's defeat, everyone mourns Alphonse's sacrifice. Edward rejects using a philosopher's stone to bring him back to life, even after Hohenheim offers his final life as an apology for the pain the Elric brothers were forced through. Edward ultimately decides to perform a human transmutation on himself, sacrificing his own gate and his ability to use alchemy with it. As a reward for discovering he does not need to perform alchemy, Edward is allowed to bring Alphonse back with him in his original body. As everyone recuperates from the battle, Hohenheim returns to Resembool and dies peacefully before Trisha's grave.

Deciding to help sort out Ishvalan policies, Mustang is approached by Knox as well as Marcoh, who offer him a philosopher's stone to get his eyesight back, though Mustang insists it be used to fix Havoc's legs first. Olivier secretly rescues Scar so that he can assist Miles in rebuilding Ishbal. Having previously seen off Ling, who had promised to take care of May's clan among others once he becomes emperor, the Elric brothers return to Resembool where Winry awaits them. Two years later, Grumman, who had become Fuhrer, visits Bradley's wife, who had been raising up Selim to be a compassionate child. Alphonse decides to travel with Jerso and Zampano to Xing and other eastern countries to learn about alkahestry, while Edward learns what he can in the west, hoping to pull their research together. As Edward heads off, he and Winry finally express their love to each other using the term of equivalent exchange.