Renton Thurston, son of the legendary hero Adrock Thurston, lives a boring, monotonous life in the village of Bellforest. This life is suddenly interrupted when the mysterious LFO known as the Nirvash Type Zero and its pilot, Eureka, crash-land into his room, followed by Gekkostate – and the United Federation military.

As Gekkostate engages the military in the sky over Bellforest, Renton attempts to deliver the Amita Drive, a memento of his father, to Eureka and the Nirvash. In doing so, he releases the typeZERO's hidden power – the Seven Swell.

The members of Gekkostate rush back to the Gekko after defeating the Izumo's KLF platoon, with Renton in tow. When they arrive to find a military blockade, the Nirvash must conduct a daring decoy operation in order to draw attention away from the Gekko.

Renton has joined Gekkostate in order to be with Eureka, but what he discovers is that life on the Gekko is not much different from his previous life in Bellforest – until Gekkostate takes a certain job in order to earn some desperately needed money. Meanwhile, the Council of Sages decides to reinstate Dewey Novak, a former military officer who has ties to Adroc Thurston and something known only as the "Ageha Plan".

Renton goes with Talho Y?ki and Hilda on a routine shopping errand, but when Talho gets drunk and into trouble, it's up to Renton to protect her by piloting a combat LFO for the first time.

Renton's relationship with the kids that call Eureka "Mama" worsens as he becomes the victim of multiple pranks. However, when the kids' latest anti-Renton adventure compromises the Gekko's stealth capabilities, Renton takes to the skies with them to disable a military outpost in the Gekko's path.

Gekkostate's hazing of Renton continues; he is sent on a "mission of utmost importance", which is a front for a drawn-out prank that eventually involves Moondoggie as well. Meanwhile, KLF squads are being destroyed and Dewey begins formulating a plan to deal with the enemy, known as Coralians.

Renton, Eureka and the kids (Maurice, Maeter and Linck) go on a shopping trip, where they meet Tiptory, a member of the Vodarac religion. Meanwhile, Gekkostate takes a job to capture a suspected terrorist – who turns out to be none other than Tiptory.

After landing at Ciudades del Cielo, an altercation between Renton and Holland Novak leads to Renton running off into the city, where he discovers the truth of what happened there and the origins of Gekkostate.

Holland hears news of a big wave arriving on the other side of the planet, so he has the Gekko take off in an outer-atmospheric flight mode to get there in time. However, Talho, irritated at what she perceives as the selfishness of the rest of Gekkostate, redirects the Gekko to the ruins of a military base that holds special meaning for her and Holland.

A Coralian appears over the town of South Ailess, and Gekkostate decides to investigate. Meanwhile, Dewey's new unit, the Nirvash typeTheEND, and its pilot, Anemone, also head towards South Ailess with the Izumo. As the two ships reach the Coralian and attempt to break through, the two Nirvashes meet in battle.

As the two Nirvashes, typeTheEND and typeZERO, unleash their power, they are drawn into the body of the aerial Coralian, known as the Zone. Inside, Renton, Eureka, and Anemone are connected by what appears to be a dream, and yet not. Renton was trapped in a dreamworld being controlled by Anemone while Eureka followed Renton inorder to get him back. Meanwhile, the Gekko and the Izumo engage in a desperate game of chicken.

In the wake of the Coralian's disappearance, Eureka and Anemone are left injured. Renton and Dominic, who showed up to pick up Anemone, travel to the nearest town to get some medicine for the two. Later, when they return, they find themselves in the middle of a skirmish between the Gekkostate's LFOs and the Izumo's KLFs.

Renton, Stoner, and Dominic mull over previous and recent events – the appearance and disappearance of the Coralian and the mutiny of the SOF members who would become Gekkostate.

Gekkostate is on a health craze and send Renton, Eureka, and Matthieu to visit Controlad on a mission to gather a certain fruit. All over town, they find the prices are too high... so they decide to pick some up “in the wild”. This gets them into trouble with a local farmer, who turns out to be Renton's uncle, Yucatan Iglasias. When Renton lies to him about being in the military, things quickly spin out of control.

The Gekko lands at FAC-51, an abandoned mine, to undergo repairs in the aftermath of the battle at South Ailess. Eureka has been silent and aloof ever since Renton piloted the Nirvash to rescue her and Matthieu from the military. While trying to find a way to interact with her, Renton is called on an expeditionary trip into the mine with Hap, Matthieu, Moondoggie, Gidget, and Stoner. Renton wanders off and finds a mysterious house.

The Gekko needs a large amount of reflection film to fix the damage from South Ailess, so Ken-Goh, Moondoggie, Hap, Matthieu, Stoner, and Renton visit a local workshop to get some made. When they arrive, they find the shop in disuse and its current owner, Neil, drunk. After Ken-Goh gets Neil to agree to make them some film, they head out to catch the raw materials – skyfish. Meanwhile, Dewey announces his plan for the world to his new unit.

While the Gekko's repairs are moving along at a steady pace, Renton meets a miner who hasn't given up on FAC-51. He begins to make friends with him when they discover a common interest. However, the miner is desperate for a big score, and when he sees the Nirvash typeZERO, he sees the biggest score of all – even if it means taking it from its current owners. Meanwhile, Eureka begins to show signs of stress from being around the mine.

Eureka's condition worsens, and Renton is lost in thought. In the midst of depression, Eureka climbs into the Nirvash and removes the Compac Drive; however, this leads to the Nirvash activating by itself. When Renton finds out, he chases the Nirvash deep into the mines. Meanwhile, the military launches an all-out attack on FAC-51, hoping to smoke Gekkostate out – or bury them under the rubble of the collapsing mine.

Eureka is brought to the medical bay in the wake of nearly merging with the Scub Coral. Tensions between Renton and Holland continue to rise, and when Holland decides to go on a rescue mission for the Vodarac over Renton's insisting that he take Eureka to a “proper” hospital, a violent argument breaks out. When the rescue mission goes sour, though, Renton still goes out to help–after getting some sense slapped into him by Talho. Renton, although while helping Holland, goes too far after not knowing about what was between Eureka and Holland.

The Vodarac priest that Holland saved conducts the ritual to remove the remnants of the Scub from Eureka's body. Renton tries to come to grips with the fact that he's been killing people in the Nirvash the whole time he's been with Gekkostate. When the members don't give him the answers he wants to hear, he decides to jump ship and run away from everything. Meanwhile, Dewey contracts a pair of mercenaries to deal with Gekkostate once and for all.

Renton wanders aimlessly after having left the Gekko, while the members of Gekkostate discuss his departure and how to tell Eureka. Eventually, Renton winds up in the city, where he meets Charles and Ray Beams. They take him aboard their ship, the Swan; after seeing how they live, compared to his former life on the Gekko, he decides to stay.

Renton joins Charles and Ray on a job to deliver a believer in Vodarac to a holy ground, but when Renton tries instead to get the girl treatment, contradicting the family's wishes, he learns more about how the world around him works. Meanwhile, Holland tries to deal with the fact that he has to tell Eureka that Renton left the Gekko.

Eureka, lonely without Renton, begins to take on his responsibilities. Holland finally admits the real reason he's been so hard on Renton. Renton, aboard the Swan, begins to feel like a family with Charles and Ray. On a test run that turns into an encounter with the military, Renton and Charles lay bare their respective secrets – that Renton was with Gekkostate, and Charles and Ray were hired to destroy Gekkostate.

After leaving the Swan, Renton once again wanders around, unable to find a way to return to the Gekko. He collapses in a forest of pile bunkers and is found by William B. Baxter, a hermit living with his wife, Martha, who suffers from Despair Sickness. As he recovers from his weariness, he learns more about nature and about love. Meanwhile, Holland searches for Renton amidst military blockades – until he realizes the Gekko is nearly surrounded.

The military prepares their assault on the Gekko, while Holland rushes back to try and extricate Gekkostate from impending disaster. However, when he shows up without Renton, Eureka takes matters into her own hands and goes out to search for him ... just as Renton returns to the Gekko, looking for Eureka.

During a lull after the failed ambush on Gekkostate, Renton and Eureka are “locked” in the brig while Holland and Talho prepare for an inevitable attack by Charles and Ray. When the attack finally happens, the plans laid by the two ex-SOF aces are played out, leading to confrontations between Renton, Talho and Ray, and Holland and Charles.

Renton tries to deal with the shock of Charles' death. Meanwhile, depressed beyond the point of sanity, Ray attempts one final kamikaze attack on the Gekko with the Spearheads and the Swan.

Dominic visits Bellforest in order to try to get information on the Thurston family. Meanwhile, Renton is still trying to cope with the Beams' deaths – and a startling revelation about Eureka.

In order to repair and upgrade the Nirvash, which lost armor plates during the military ambush led by Charles and Ray, Gekkostate prepares to land at Tresor, a military research and development facility. While there, Renton learns a bit about Eureka and the typeZERO's pasts, and Talho decides to change, on the inside and outside, along with Holland.

Coda, one of the Sages, descends to the planet to meet with Dewey concerning his Ageha Squad. Meanwhile, the typeZERO rejects its current repairs; in order to design a new outer shell for it, Gekkostate must meet with the eccentric researcher, Dr. Greg Egan. When the Ageha Squad tests their new weapon outside Tresor, though, Gekkostate scrambles to finish their business there.

Axel Thurston is tasked with the construction of the Nirvash's new ref board. At the same time, following the devastation left behind by the Coralian attack, the military sends TheEND to observe the Coralians, only to get sidetracked by the Gekko.

Gekkostate takes a short break at a popular lifting spot after the destruction caused by the Coralian attack. Renton searches for memorabilia in order to try and cheer up Eureka, while Holland and Talho learn the location of Master Norb and make plans to assault the capital to rescue him. Meanwhile Holland and Talho confront the feelings they have for one another.

As the Gekko prepares to make a trajectory flight to the capital, Holland takes Renton aside with Eureka and tells him about his past with Eureka in the SOF (Special Operations Force) and his meeting with Master Norb in Ciudades del Cielo. Meanwhile, Norb meets with Dewey in the capital and the two debate the future of the planet, and Talho has a secret to reveal to Holland.

Gekkostate launches a full assault on the capital in order to rescue Master Norb. Dewey dismisses the attack as fruitless, confident that Holland would never find a partner for Eureka. In the midst of the battle, Eureka breaks off with the Nirvash and hides with Renton, unwilling to take more lives. After Talho gets the information on Norb's current position, Holland heads out to retrieve the monk and confronts Dewey in the process.

Following Norb's rescue, the monk advises Holland to hurry and take him to the Vodarac homeland if Renton and Eureka are attracted by their true feelings. Eureka sees Renton repaint over a scratch on the Nirvash and realizes how badly her own face is scarred. In a meeting with Gidget, Eureka becomes determined to try and use makeup to “look pretty for Renton”. Meanwhile, Holland takes Renton aside to tell the boy yet another story from his past; the story of his relationship with his first love, Renton's sister, Diane Thurston.

As Gekkostate records an interview with Norb and Dr. Bear in which they discuss the military's plans and the "Limit of Questions" theory, Dewey stages a show of his own for the media and accuses the Sage Council of standing idly by while the Coralians assault human civilization. Dewey promises the public hope in the form of the Ageha Squad, using Adroc Thurston's name to sway the world.

When Renton learns that Eureka knew his father before he died, he becomes upset and the two fail to communicate their feelings properly. The tension between them is misunderstood by the rest of the Gekko's crew, some of whom believe Renton wants to or tried to have sex with Eureka. Meanwhile, at the capital, Dewey finally makes his move against the Sage Council.

While the Gekko is refueling for the final leg of its journey to the Great Wall, Norb orders Gekkostate to play a game of futsal. Tensions are high on the soccer field as many of the crew question Norb's motives. At the capital, Dewey blames the death of the two sages on the Coralians, and prepares an attack on the Great Wall in retaliation.

Gekkostate finally arrives at the Vodarac shrine, very near the Great Wall. However, in order to pass through the Great Wall, Norb explains that Renton and Eureka must first infiltrate the shrine and meet with Sakuya. Dewey orders the deployment of military forces to the Great Wall, including his new flagship, the Ginga.

Eureka enters the strange lotus bud they find at the core of the Vodarac shrine, and inside finds a library much like the one she found when she nearly merged with the Scub Coral. Inside this library, she meets Sakuya. Norb tells Renton (and Sakuya tells Eureka) the story of how the two fell in love and attempted to pass the Great Wall. Outside, Holland's group defends the shrine against Vodarac soldiers, with the UF military approaching fast.

Dewey launches an attack on the Vodarac shrine and uses Orange to summon a Kute-class Coralian. Renton, Eureka, and the kids race towards the Great Wall in the Nirvash, with the Gekko and its LFOs covering them. Amidst the antibody Coralians and Federation ships, Anemone and TheEND launch to pursue typeZERO into the Zone.

Renton, Eureka, and the children find themselves stranded on humanity's former home, Earth, with no idea where to go or what to do. As Holland boards a new LFO and fights alongside an upgraded Gekko against the military's AFX ships, Dominic kisses Anemone. Afterwards Dewey takes Anemone to a New Year's ball and tells her the story of his childhood. Meanwhile, Dominic is given a new order: to head to Warsaw with Jurgens and the Izumo in order to select the next pilot of TheEND.

Dominic arrives at Warsaw with his orders from the last episode, and finds a facility that performs experiments on young girls with desperation disease. However, the experiment ends in the death of all three specimens, and Dominic is forced to inform Dewey that there was no replacement for Anemone. Meanwhile, stress continues to take its toll on Renton's group as they explore Earth, and Eureka's condition grows more dire. Note: This episode was rated TV-MA-V

Dominic and Jurgens arrive at Tresor under their orders to capture Gekkostate, but rather than carry them out they demand a talk with Dr. Bear in order to ascertain the truth of Dewey's plan. Meanwhile, Renton chases down Eureka and confronts her about her transformation, with the kids right in the middle.

Dewey at last discovers the location of the Scub Control Cluster. As the military launches all over the world, ref boarders and DJs relay information on their activities to Tresor. Holland and Jurgens quickly ready their crews for battle. On Earth, Eureka and the kids tend to Renton's fever, and Eureka undergoes yet another transformation.

Renton reunites with his sister Diane shortly after he, Eureka, and the kids discover the Control Cluster. She tells him the history of Earth and the Scub Corals, leaving him and Eureka to make a very important decision about humanity's future.

Dewey's plans come to fruition as he creates a hole in the Scub Corals, sending Anemone to the Control Cluster to target it for destruction. With the opening closing fast, Dominic tries to find Anemone before she completes her suicidal mission.

The Control Cluster has been destroyed along with TheEND, and the typeZERO is badly damaged. Debris from the destruction of the Oratorio #8 are carried on trapar to towers around the globe, while Dewey enters the Scub Coral to destroy the last hope the world has: Renton, Eureka, and the Nirvash. Holland confronts his brother on the Ginga, but Dewey has one last trick, and it may cost Eureka her life...

Eureka is becoming the next Control Cluster and all hope seems lost. The Nirvash can't be operated and surrounding Eureka are millions of antibody Coralians. The Gekko prepares for one last mission, but can Renton summon the strength to save the one he loves?

April 2025 on the Okinawa Islands. 13-year-old Ao Fukai, is hanging out with his childhood friend, Naru Arata, until he takes her home. He accidentally takes a bracelet being smuggled by Gazelle, Pippo, and Han Juno, and a Scub Coral suddenly appears, along with a G-Monster/Secret. Gazelle and his friends were smuggling the item to the Japanese Armed Forces, but they discover the bracelet is missing and go to find Ao to try to retrieve it. In the interim, another Scub Coral and G-Monster appears, as Cristophe Blanc of Generation Bleu makes a deal with the Union of the Okinawa Islands government to take care of the new G-Monster. Ao soon realizes that the bracelet is one owned by his long-lost mother, Eureka, years ago and refuses to give it up just as Gazelle goes to take it back.

The G-Monster continues its attack on Iwato Jima, and with Gazelle's help Ao pilots an IFO being transported by the Japanese Navy and uses it to defeat the G-Monster, his hair changing from brown to turquoise in the battle, all while Team Pied Piper pilots watch, realizing that the IFO is the first ever model made.

Ao is hunted down by the people of Iwato Jima because they still believe that he and his mother are to blame for the terrible accidents that befell the island when she appeared out of nowhere. While in the custody of local musician Kazuyuki Kinjo, Kinjo apologizes to him for what his generation has done, just as Ivica Tanovich of Generation Bleu seeks him out, realizing he is the pilot of the Nirvash. While Rebecka tries to convince the Okinawa Self Defense Forces to allow Team Pied Piper to get rid of the Scub Coral, another massive Secret appears to attack. Gazelle frees Ao who brings the boy back to the Nirvash, which he realizes must be the IFO piloted by his mother Eureka, and that he was the one meant to pilot it in her absence.

With renewed resolve to protect Iwato Jima, Ao takes on the G-Monster with some help. And in the aftermath, Ao begins to learn that the world is more complex than he realized. Flying to the world's largest Plant Coral in Okinawa, Ao meets up with Naru and Ivica, who tells him about Eureka's disappearance. In hopes of finding his mother and learn more about his birth, Ao decides to join Generation Bleu.

While adjusting to life in Generation Bleu, Ao begins to feel uncertain about why he joined them in the first place. Meanwhile, Team Goldilocks is under attack during an operation.

Team Pied Piper is dispatched to aid Team Goldilocks, but upon their arrival, they find that their leader sacrificed himself to save his companions. After retrieving the pilots and their IFOs, they return to confront the enemy Secret leaving an exhausted Ao behind. After waking, Ao hears from Chloe, one of Goldilocks' pilots about their battle with the Secret and comes up with a plan to defeat it. While Ao confronts the Secret, he is watched by an enigmatic figure who takes an interest in him.

The stranger, who calls himself "Truth", invades Generation Bleu's headquarters in search for the Nirvash. After having a confrontation with him, Ao is knocked unconscious and dreams about Truth approaching Naru and disappearing with her. After waking up, Ao is informed that Truth was indeed at Iwato Jima and has kidnapped Naru.

A Secret appears in the Republic of Faisal Arabia, but on behalf of its own interests, the United States government forces Generation Bleu to not engage it. Ao's comrade Fleur Blanc reveals to him the reason why she hates her father, Generation Bleu's president Christophe Blanc, but he manages to cheer her up and both return with renewed spirits to battle when they are finally authorized to confront the enemy.

The Japanese government runs an experiment in Tokyo Bay trying to create its own Plant Coral. However, a Secret appears and starts wreaking havoc. Team Pied Piper is dispatched to the area, but when Ao is informed that protecting the city from the Secret is not their top priority, he leaves against orders to engage it.

A Scub Burst appears in Phoenix, Arizona, and while Team Pied Piper is on standby waiting for an official authorization to intervene, Ao and Ivica go ahead to evaluate the situation. As they arrive, Ao meets Truth once more, holding a group of survivors hostage while the US Army comes up with a different approach to confront the enemy Secret with disastrous consequences.

Team Pied Piper returns from a mission in Australia, unaware that they have brought with them a sand-like substance that makes the child pilots have strong hallucinations. Meanwhile, Gazelle and his friends investigate the past of Ao's fellow pilot Elena Peoples just to discover that she is even more mysterious than they previously imagined.

Team Pied Piper goes to a Generation Bleu space station to deposit the collected Quartz. While there, a Secret attacks a Scub Coral that has materialized in low orbit, and Team Pied Piper is sent out to intervene. Meanwhile, Truth begins to set his plan in motion, and Gazelle and his friends investigate the area beneath Generation Blue HQ, discovering the Coral Relic. When Ao manages to destroy the Scub Coral in orbit, it turns out to have the Gekko inside of it with the Nirvash Type0 piloted by Ao's mother Eureka.

On board the Gekko, Ao discovers that the Eureka before him is a past incarnation of her, from the time she was still pregnant. Soon, the ship is surrounded by the Japanese and Okinawan armed forces, all desperate to take possession of both the past Eureka and her Nirvash. While trying to figure out how to send Eureka back to her own time, Ao and the others are attacked by Truth.

Despite Truth's intervention, Ao manages to return Eureka to her proper time. He then hears from her that the baby she is carrying is not a boy, but a girl, meaning Ao has an older sister. After returning home to find more about his sister, he learns from his grandfather Toshio that Naru reappeared, but upon reuniting with her, the Japanese government declares claim of Iwato Jima and blames Ao for the death of one of its officers.

Uneasy after his last encounter with Naru and Eureka's claim that the Secrets are not enemies, a sleep-deprived Ao is sortied along his team to confront a Secret which has appeared beside a Scub Coral that was mysteriously reactivated. Ao is shot down by the enemy and after waking up, he learns that the other Scub Corals around the world are being reactivated, too, putting Generation Bleu in a state of maximum alert to confront the multiple Secrets emerging near them.

Several countries join Generation Bleu's special 'Polaris' operation to lure all Secrets that have appeared around the world to a deserted area in the Arctic and destroy them. The plan goes well, until Truth interferes changes its course above Norway's Plant Coral, and Ao takes the initiative to ensure that the operation ends with no civilian casualties. After disposing of the Secrets with his newfound weapon, the Quartz Gun, Ao learns that his actions changed history, and he is the only one who realizes that.

Ao confirms that the members of Team Goldilocks are living ordinary lives as if they were never assembled at all. However, the public opinion starts turning against Generation Bleu and during an operation in the middle of the ocean, the Quartz Gun starts moving by itself. Han Juno concluded the book of Johannson, who believed the existence of another world: where their world human population is around half of its original number, Okinawa became an independent nation, and the Soviet Union still exists in their realm. Ao confronts Truth and has a brief encounter with Eureka who reveals to him the reason for her disappearance.

To protect his comrades, Ao surrenders himself, the Nirvash, and the Quartz Gun to the U.S. Army. With the whole world in doubt regarding Generation Bleu's intentions, Fleur and Elena decide to launch an attack on the carrier where Ao is being held to bring him back.

Furious upon hearing that he is actually a Secret who has lost his memories, Truth destroys Generation Bleu's space station among thousands of satellites around the globe. The Allied Forces blame Generation Bleu for the incident and launch an attack against them. Truth takes the opportunity to infiltrate the base and attempts to steal the Quartz Gun, but is stopped by Cristophe who sacrifices himself to allow Ao and Fleur to escape.

After learning that both Elena and the members of Team Harlequin switched sides to join the Allied Forces, Ao and his friends manage to escape, taking the Quartz Gun with them. With nowhere to run, the remaining members of Team Pied Piper are contacted by the Japanese government offering them shelter and support according to a deal Cristophe made with the Secrets before his death.

Team Pied Piper, the Japanese Government, and the Secrets join forces to prevent the Allied Forces from claiming the Scub Corals' Quartzes. While Naru rallies supporters for her cause of having the Plant Corals shut down, Elena joins the Allied IFO squad along with Maggie Kwan, but Eureka appears before them and makes Elena remember the truth about her origins from 1981 that she wanted so much to deny. Soon after, both are dispatched to fight Ao, and when he manages to finally dissuade Elena, Truth appears before them.

Truth attacks Ao, who is rescued by Naru when she teleports him and the Nirvash to her side in Okinawa. Reunited once more, Ao and Naru discuss the situation when Team Harlequin appears and reveals that Truth's current form can kill all people infected by the Scub Corals who approach him. As he is the son of a Coralian, Ao should stay away from him. Regardless, Ao decides to join his companions against Truth. Meanwhile, back in Eureka's timeline, her husband Renton Thurston boards the original Nirvash in an attempt to rescue her.

Truth and Ao fight for the Quartz Gun until it fires once more, erasing Truth and converting Ao's Nirvash into the “Nirvash Neo”. It also rewrites history once more to render it such that Generation Bleu defeated the Allied forces including Naru. As Naru is being hospitalized, Ao witnesses the Nirvash Spec V3 coming from the pillar and encounters it, meeting his father Renton for the first time.

After having a brief encounter with the phased-out Eureka, Renton sets with Ao to Iwato Jima where he thanks Toshio for taking care of his family and then decides to make use of the Quartz Gun to destroy the original Scub Coral at his timeline and prevent it from spreading itself throughout the dimensions. As Ao confronts him to stop it, he learns that surprisingly, Truth has not fully disappeared, but has become the Nirvash Neo's archtype instead. Ao also learned that his older sister had died soon after she was born. He then decides to make use of the Quartz Gun's last shot to negate the Secrets' existence to change Eureka's fate and have her reunited with Renton. Because of this, Ao is transported to the year 2027 where he bids farewell to Truth.