Tony Stark travels to Japan to supervise the construction of an Arc Station with Dr. Chika Tanaka (the supervisor of Lab 23 of Stark Industries' Japanese branch) and meets with Minister of Defence Kuroda who asks about Tony retiring as Iron Man and that the Iron Man Dio armor will be mass-produced for the possible recruits. The next day, reporter Nanami Ota and photographer Ichiru Masuda are told by Editor Homura to get a scoop on Tony Stark before the Tokyo Journal's competition does. Tony and Kuroda meet the three test pilots hoping to pilot the prototype Iron Man Dio armor which will replace Tony when he retires from being Iron Man. In a battle test, the armor withstands the tank attacks. Tony later holds a public event to show off the new model with him testing the Iron Man Dio armor. During the flight test, something goes wrong with the Iron Man Dio armor and it crashes near Nanami's car. Tony gets a ride home from Nanami who interviews him while Chika and her men recover the prototype Iron Man Dio armor. Tony tries to figure out what went wrong with the Iron Man Dio armor as he tells Chika to run a diagnosis on the prototype Iron Man Dio armor. When one of the pilots tests it later, he gets brainwashed and attacks the other two pilots. Upon figuring out that the prototype Iron Man Dio armor is hacked by an outside source and escapes from the facility, Tony equips his classic Iron Man armor and manages to defeat it. However, he is attacked by a strange mechanical warrior named Scorpio who comes from an order called the Zodiac. Tony defeats him, but the prototype Iron Man Dio armor goes missing having been removed from the test pilot.

A shipment of plutonium is stolen by mysterious people. The next day, Nanami is writing the article when she hears about Tony being subpoenaed to the Diet of Japan. The stolen plutonium leads Tony to be accused of smuggling nuclear materials into Japan with the ship being associated with Stark Industries and having to give a statement before the Diet of Japan claiming that the claims of him smuggling plutonium is a lie. In order to get away from the press, Tony hitches a ride with Nanami Ota and Ichiru Masuda. Nanami states that Tony still owes her an interview and wants to help improve Tony's image. While investigating the ship where the plutonium was being transported, Iron Man encounters a Zodiac robot called Cancer. Tony contacts Kuroda stating that Zodiac is behind the plutonium theft yet Kuroda doesn't want Tony to continue his investigation. Hacking into a surveillance camera, Iron Man discovers who the culprits are and loads their coordinates into the Iron Man armor. Tony Stark drives past Nanami who ends up pursuing Tony in order to get an interview and borrowing Ichiru's camera while borrowing a man's scooter. Tony has Kuroda tell the Mayor of Kyoto apologize for the traffic jam he's about to cause and catches up to the culprits. Nanami crashes into the culprit's car causing a mix-up. Tony drives them towards a security checkpoint, but he is blocked off by a JSDF operative named Captain Nagato Sakurai. Nanami mixes her camera with the plutonium the culprits were carrying to the rendezvous point and is chased by an armored tank equipped with stealth camouflage that is being piloted by the culprits. Tony Stark becomes Iron Man and goes after the tank as Nagato Sakurai sends a transmission to have the roads cleared. After Sakurai helps Iron Man deal with the tank, Iron Man faces off against Cancer again who targets Nanami for the plutonium and breaks off his claws. Iron Man then throws Cancer into the air and destroys him with his laser beams. Tony Stark is cleared of all charges and Nanami was able to write a good article. Nanami hopes that the Japanese public will learn something about this. Ichiru gives Nanami some flowers which were shipped to him by Tony Stark. Kuroda asks Nagato Sakurai about what he thinks about Tony Stark. Nagato arrives where a new armor is being built.

Strange tornadoes are appearing in Tokyo, targeting and killing Professor Ohno. Dr. Chika Tanaka gives Tony Stark a tour of the Arc Station when she gets a call from Professor Satoshi Yamaguchi that Professor Ohno is dead and loses contact with him. Meanwhile, Editor Nomura is shown an article by Nanami about Satoshi Yamaguchi being killed by a tornado. When another tornado attacks a military base, Iron Man enters it and finds the cause, another Zodiac warrior named Aries who easily defeats him. Meanwhile, Nanami attends a meeting with Dr. Chika Tanaka and Professor Michelinie. Professor Michelinie talks about the Tesla Project, an anti-natural disaster machine worked on by them and the other professors. Just then, Chika, Nanami and Professor Michelinie are attacked by the tornado which results in the death of Professor Michelinie. Tony Stark tries to help some survivors, but is met with harsh criticism from the rescue team leader Nakai who tells Tony to leave. Tony tells the rescue team leader that he has the resources to help them only to be told by Nakai to get lost. Dr. Chika Tanaka and Nanami appear outside of the house. Tony tries to help the rescue workers and ends up coming to the aid of the rescue workers when a bus starts to go under. Tony dives into the water to save the surviving bus passengers. As Chika and Nanami research the Tesla Project, they soon learn that Professor Michelinie (who turns up alive) is the man responsible for selling the Tesla research to the Zodiac and holds them at laser point. Thanks to Nanami, Chika and Nanami manage to escape. Meanwhile, Tony Stark emerges upon saving the bus passengers. While checking on the status of the Iron Man armor, Tony is shown an updated version of the EMP cannon by Chika when Chika is told that 2 F-5 tornadoes Yokasuka Base where Professor Michelinie is witnessing this as he is sucked into the tornado. With his armor repaired, Iron Man re-enters the tornado and defeats Aries with an EMP cannon. As Iron Man starts to fall, he is told by Chika to reboot the Iron Man armor. The Iron Man armor reboots as Aries crashes to the ground.

Tony recalls five years ago when he testing the Screamer jet. While in the Middle East, Tony's helicopter is shot down with Tony receiving life threatening injuries. Agreeing to make weapons for the terrorists led by Righella, he was saved by fellow prisoner Ho Yinsen who installed a magnetic chest plate to keep him alive and helped him realize the deaths his weapons manufacturing has caused. This led to the creation of the mini arc-reactor. When Yinsen asks if he ever thought of the people he has hurt from the weapons he has made. After making an updated mini arc reactor, Ho Yinsen flips a coin to decide if he should help Tony. This leads to Yinsen helping Tony into building a device that would get Tony Stark and Yinsen managed to create the first Iron Man armor. When a terrorist soldier comes in, Tony finishes the armor's power-up as Yinsen sacrifices himself to give Tony a chance to escape. Tony emerges in the armor knocking out Righella as Yinsen tells Tony that this is as far as he goes and to finish what he has started. Meanwhile in the present, Tony remembers his five-year anniversary. A race driver named Kawashima had broken his legs and desires to race again after his meeting with Nanami after being told that he will never race again. At a banquet, Dr. Chika Tanaka learns on why Tony Stark has changed his company from a weapon company to an industrial company. Meanwhile, Kawashima is approached by a mysterious person from Zodiac and states that he can receive cybernetic enhancements from Zodiac on the condition that he kills Tony. While at the race tracks, Tony is visited by Nanami Ota who states that she is here when Kawashima has returned to the race tracks. When Tony is targeted, he is saved by the sudden appearance of Logan (who is in Japan investigating A.I.M.). Kawashima emerges as a cyborg and flees. Wolverine tells Tony that the Zodiac is turning humans into cyborgs. The next day, Tony is followed by Nanami as Tony changes into his Iron Man armor. Nanami wants to help Iron Man find Kawashima who ends up showing up. Kawashima summons the Zodiac warrior Taurus which he pilots into attacking Iron Man. Taurus soon starts to take over Kawashima. With the help of Logan, Iron Man defeats Taurus and rescues Kawashima as Nanami rushes Kawashima to Lab 23 as Iron Man's computer detects Iron Man Dio approaching. Iron Man soon comes face to face with Iron Man Dio. As Iron Man is shot down, he recovers and states that he wants the Iron Man Dio armor. Iron Man is shocked to find what appears to be Yinsen inside who ends up leaving saying a word.

After testing a space armor testing, Tony has Pepper Potts do a background check on Ho Yinsen. An Arc Station Worker is brought in with a strange virus in which people's bodily fluids are turning blue and Tony is told of this by Chika. Nanami and Ichiro then bring in a high school girl who has also come down with the virus. Nanami calls Tony stating that the virus has turned into an epidemic spreads across Tokyo as her call is watched from a distance by someone that looks like Yinsen. The JSDF suspects that the Arc Station is causing it and Kuroda and the Minister of Health have the JSDF puts Tony under watch. He is approached by Sakurai who informs him that a satellite named SAT-1 has been taken over by a Zodiac warrior which is causing the radiation. Meanwhile, Nanami also gets sick from the radiation. Using an experimental coating to protect him from the radiation and a special armor, Iron Man launches into space with the help of Sakurai to face the Zodiac. However, he is at a disadvantage in zero gravity and is taken inside the Zodiac where he is exposed to high radiation. Chika and the JSDF lose contact with Iron Man. However, Iron Man manages to send the radiation data back to Earth so they can cure the victims. Iron Man breaks free from the Zodiac and destroy it. With the infected patients cured, Iron Man flies back to Earth stating that they still have a score to settle with Zodiac.

A week after the epidemic caused by Zodiac, Tony is told by Pepper Potts that someone that looks like Yinsen was sighted on the streets yet there is no official confirmation on this. As Pepper looks into this on her end, Lab 23 is attacked by the Pisces Virus which causes the robotic cleaners to go berserk and greatly reduces the temperature in the complex. Tony and Chika try to shut out the Pisces Virus with a firewall, but this allows the Pisces Virus to infect computers around the city and even takes over some fighter jets. Meanwhile, Editor Nomura calls up Nanami stating that the train computer systems have caused a derailment as she states that there are some glitches on their end as well. The Pisces Virus has also causes the ATMs to emit a lot of money as Nanami receives a text on her cell phone that says that it will fight for the weak. The Pisces Virus also affects some of the JDSF as Kuroda doesn't want Sakurai to dispatch Ramon Zero. Tony gets an E-Mail from the Pisces Virus owner stating that he will stop the evilsof Tony Stark. In order to lure the culprit out and protect the Arc Station, Tony takes the Pisces Virus into the Iron Man armor in order to fight it. Hearing Tony's promise to protect people, the culprit who turns out to be a boy named Sho (who was approached by the same Zodiac operative that approached Kawashima) is reminded of his promise to his late mother Maria to protect others. This causes Sho to delete the Pisces Virus and do what he promised to his mother. As Iron Man's armor returns to normal, he is attacked by two Zodiac Cancer robots. Just then, Iron Man is saved by someone piloting a new armor called Ramon Zero.

While wondering about the mysterious new armor, Tony finishes his shower and spots Chika outside. When going out towards Chika, Tony is hit by a tranquilizer dart as he and Chika are kidnapped. Following an interview, Nanami spots Tony's car and attempts to follow it, but he and Ichiro are stopped by a Zodiac. When they find Tony's car, they find him gone and spots a yacht as Nanami reports suspicious activity. On a boat, a mysterious Zodiac operative works on Tony Stark. Tony and Chika awake to find themselves on a remote island near Japan that has been used for landfill and Tony's arc reactor is missing. While exploring the island, they are approached by Yinsen who reveals himself to be a member of Zodiac and that the Yinsen he knew is dead. When Tony states that Yinsen wouldn't side with Zodiac, Yinsen tells Tony he has 24 hours of pacemaker power to decide whether or not he wants to join Zodiac stating that they need a man with his talent. Yinsen then leaves stating that Tony shouldn't waste his time trying to escape. Tony and Chika attempt to use the various scrap on the island to find a method of escape when Chika's cell phone has no reception. Tony connects Chika's phone to a laptop he found on the island only for them to receive a transmission from Yinsen stating that all wireless signals within the radius of the island are jammed. When asked by Tony what made Yinsen flipped, Yinsen states to Tony that he should make the time he still has to join Zodiac or not. While on his boat, Yinsen thinks to himself stating that he will unlock Tony's real him and determine if Tony hasn't broken his promise to him. Zodiac's leader then contacts Yinsen about Tony as Yinsen is researching Tony's arc reactor. Tony and Chika rig up a boat only for them to attacked by another Scorpio robot and knocked off the water. Upon making it to shore, Tony states that he won't be helpful without his arc reactor. Chika states that despite the situation, Tony manages to find a situation. Tony tells Chika that he saw a yacht that Yinsen might be on before Scorpio attacked. Tony states that he must show Yinsen he change and find a way to fight. Meanwhile, Nanami tells Nagato Sakurai about what happened the night when Tony and Chika were kidnapped. Sakurai asks which way the boat went as Ichiru shows the image that fell on Namai's car. Yinsen has Scorpio give him a visual on Tony. When he finds Tony building something, Yinsen tells Scorpio to fire on Tony Stark. Tony and Chika eventually manage to evade Yinsen and Scorpio robot by using a hologram as Scorpio is ordered to eliminate Tony. After a talk with Chika where she is left someplace safe, Tony forges his own rocket. Scorpio manages to corner Tony who prepares to use a flare. When Yinsen hopes that Tony will use the rocket on Scorpio, Tony shoots the rocket into the air which is enough to alert Ramon Zero. Ramon Zero manages to destroy the Scorpio robot. Impressed by Tony not using weapons upon him and Chika making it towards Yinsen's yacht, Yinsen returns the arc reactor to Tony stating that this was just a test. Before escaping in the Iron Man Dio armor, Yinsen states that next time Tony won't be so lucky. Ramon Zero is revealed to be Sakurai who states that he should thank Nanami for her part in the rescue and leaves. As they wait for rescue, Tony and Chika kiss each other after thanking Chika for her help.

While being curious about why Chika is turning down his date requests, Tony encounters a telekinetic girl named Aki who claims to have escaped from Zodiac and is asking for protection. While at a restaurant, Aki shows Tony her telekinetic abilities and asks Tony if she believed that she escaped from Zodiac. When asked if Zodiac sent Aki, Tony tries to keep her from crying. At a warehouse, Sakurai is shown that some of his men were killed securing a warehouse. Later that night, Tony calls up Nanami to do some research Aki. The next morning, Aki ends up cleaning up Tony's house and shredding some important documents. Tony has trouble with Aki wrecking his lab and his relationships with Chika. Aki retaliates by using her telekinetic powers to knock Tony into a wall. With some info Nanami dug up from Aki at an orphanage, Tony learns that Aki's parents died two years ago when the airplane she was on was hijacked and exploded. Following the accident, Aki was adopted by a strange group six months ago. Nanami tells Tony stating that she wasn't the first who came asking about Aki. Tony catches up to Aki at a nearby soccer field where she states that her powers went out of control and caused their hijacked plane to crash. Later that evening, Sakurai arrives and takes them both into custody. Tony suspects that Sakurai was the one who asked about Aki as he is tasered by Sakurai. While on a JDSF van, Tony is told by Sakurai that Aki's powers can manipulate the iron within someone. Sakurai states that Zodiac plans to use Aki's abilities for their own use. Just then, the van they are in are attacked by the Zodiac warrior Virgo. While the JDSF fight Virgo, Tony ends up getting Aki to Lab 23 upon borrowing a motorist's car. After admitting Aki into Lab 23, Iron Man goes to battle Virgo while Chika discovers an anomaly in her scan while Chika researches the flashdrive. Iron Man soon learns from Chika it is synchronized with Aki's brainwaves, meaning destroying it would kill Aki. Aki gets up in order to help Iron Man as the fight is taken to a local park. Aki arrives and uses her powers to block Virgo's attack. Sakurai arrives in the Ramon Zero armor to fight Virgo as Iron Man blocks the attack bound for Virgo. Aki is knocked out as Virgo drags Aki into it. Chika orders her workers to arm the EMP Shields to protect the Arc Station from Virgo's attack. Sakurai asks Iron Man if his plan would end up harming people. Iron Man breaks through the shield to shut down Virgo and rescue Aki. Chika orders the workers to drop the EMP shield and to destroy Virgo's residual energy. It is revealed that Aki loses both her powers and her memories but is much happier as Tony and Chika watch her play on the soccer field.

While in his hideout, Yinsen recalls the time when he was saved from death by a woman named Shehla who discovered Yinsen's body. Yinsen then gets a call from Zodiac's leader who tells Yinsen that an opportunity has come up for him. Meanwhile, Tony is nearly finished with his arc reactor, but Yinsen apprehends the shipment of plutonium needed to complete it using the Iron Man Dio armor. Sakurai is told by a JDSF operative that his clearance to use the Ramon Zero armor has been denied. Iron Man and Yinsen battle before Yinsen escapes with the plutonium, leaving Iron Man to fight the Zodiac warrior Sagittarius, but he soon loses him. Tony speaks with Kuroda who states that Japan was attacked twice as Tony vows to get the plutonium back. After Tony is told by Sakurai that Ramon Zero has been cut off from him, Tony is then contacted by Yinsen who tells Tony that the people who rescued him were killed by Stark Industries weaponry and how he was approached by Zodiac's leader who convinced him that Tony Stark hasn't changed. The two once again fight for the plutonium with Yinsen insisting that Tony has not changed. He reveals several models of Iron Man Sigma which he created by reverse engineering the Iron Man Dio armor and uses to attack the Arc Station as Chika, Nanami, and Ichiru are among those at the Arc Station that are taken hostage. Yinsen defeats Tony, takes him out of his armor, and throws him into a river. Yinsen then arrives at the Arc Station to begin his new world order.

After taking over the Arc Station and holding some people hostage, Yinsen forces Chika to work on the arc reactor as he shows her Tony's Iron Man armor. Yinsen then makes his demands for the dissolution of the Armed Forces and National Diet. Nanami attempts to escape the hostage situation, but is caught by Yinsen and a Zodiac guard and thrown into a storage room. Tony is rescued from the river by Sakurai and tries to contact Chika, but she is caught by Yinsen and throw into storage with Nanami. Meanwhile, Kuroda offers to be held captive in place of the hostages. As Chika and Nanami go through an air duct and retrieve Tony's armor, Tony and Sakurai are attacked by Sagittarius. Nanami gets the armor to Tony so he can defeat Sagittarius, before facing off against Yinsen. Just as Iron Man starts to get the upper hand when Yinsen hesitates attacking in front of Chika, someone overrides the Iron Man Sigmas and attacks them both, with Yinsen getting critically wounded. After Iron Man destroys the Iron Man Sigmas, Yinsen apologizes for his actions and not knowing that the Zodiac corrupted him. Yinsen then warns Tony that the Zodiac's plan has just started.

Although the hostage situation was brought to a close, Tony is suspected of having links to Zodiac and is arrested by the JSDF. Sakurai briefly takes him to his home where he teaches him how to control his ego. Meanwhile, Chika is somehow controlled into overloading the Arc Station, which causes power outages in various facilities which are then taken over by Zodiac who then attack the National Diet. They then send a message saying they have taken control of the government and claim Tony is their ally. Kuroda orders Sakurai to kill Tony, but Tony escapes and learns about the power regulation from Chika, who tells him that power is being directed to Tokyo Bay before she is taken hostage. As Iron Man heads towards the location, he is attacked by Sakurai in Ramon Zero, but Tony manages to snap him out of it before they are attacked by another Zodiac mech. While Iron Man fights the Zodiac mech, Sakurai heads to the location and discovers Zodiac's weapons factory also learning their leader is Kuroda, who plans to rebuild Japan as a military nation. Sakurai destroys the factory but is killed by Kuroda using his Rasetsu armor. After Iron Man fends off the Zodiac mech, he receives a final transmission from Sakurai telling him that Kuroda is the leader of Zodiac before he dies at the bottom of the harbor.

Kuroda enacts a coup d'etat and declares martial law over Japan. Meanwhile, Chika admits to Tony that she's been having blackouts and has been controlled into altering the arc reactor, wanting to commit suicide for causing Tony's suffering. Just then, Kuroda approaches them in his Rasetsu armor and takes control of Chika (who had really been a Zodiac warrior) and transforms her into her Zodiac form (the same one that Tony fought in the last episode) to have her attack Tony. As Tony tries to get Chika to believe in herself, she stabs herself to break free from Kuroda's control. Tony leaves Chika in Nanami's care while he goes to fight Kuroda, who was resentful due to his grandparents being killed in the Nagasaki bombing. Meanwhile, Chika decides to transfer her consciousness into the arc reactor program in order to take control of it and transfer its energy over to Iron Man. With the massive power provided, Iron Man unleashes a massive Unibeam that completely obliterates Kuroda, but Chika dies as a result of the transfer. A month later, the Chika Tanaka Memorial Arc Station is finally activated providing clean energy for the entire world and Tony is seen returning to America.