Tony Stark arrives in Japan with the aim of setting up the Arc Station as the first step of his World Peace Initiative. In front of all of Japanese citizens, he announces his new Iron Man model, Iron Man Dio, with himself in the pilot's seat. However, during the demonstration, Dio crashes due to a mysterious bug in its operating system. Later at Lab 23, the Dio armor takes over its human pilot and begins to attack the facility. Tony is forced to pull his original Iron Man armor out of retirement and chase after Dio; before he can catch his breath, the Zodiac warrior Mech Scorpio appears.
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Tony Stark is accused by Defense Minister Kuroda of sneaking plutonium into a Japanese undefended cargo ship. This ship has been attacked and the plutonium has gone missing, posing a grave threat to the country. Suspecting that he's been set up, Tony dons the Iron Man armor and vows to retrieve the plutonium to clear his name. He tracks down the stolen nuclear material and discovers that Zodiac, a terrorist group associated with Advanced Idea Mechanics (A.I.M.), is behind this theft. Attempting to get Tony's attention, reporter Nanami Ota gets caught up in the chase and nearly killed. Iron Man ultimately defeats the Zodiac warrior called Cancer, and retrieves the plutonium while Nanami finally gets to write her first story on Tony Stark.
Nanami is trying to get to investigate the terrible hurricanes that have killed two notable scientists. Her search takes her to Professor Sakamoto, and his former student, Dr. Tanaka. Sakamoto and Tanaka, who were once involved in the Tesla Project – a project that aims to manipulate weather. Is the Tesla Project related to the weird weather attacking Japan? Even if they are, what can Nanami do to stop it? Can Iron Man defeat the weather?
Tony Stark is supporting a charity racing event in order to burnish the image of Stark Industries. He explains to Dr. Chika Tanaka on how his encounter with Dr. Yinsen after his kidnap changed his perspective of life and inspired him to work for world peace. Meanwhile, A.I.M./Zodiac has approached Kawashima, a race car driver who is suffering from career-threatening injuries. The terrorist organization promises Kawashima that they will cure his injuries if he takes out Tony Stark. When Tony makes an appearance at the race track, Kawashima tries to kill him with a test car. However, Logan, the mutant X-Man known as WOLVERINE, shows up save him just in time. Logan also gives Tony some crucial information about A.I.M. They track Kawashima down and find him operating in the Zodiac killer Mech named TAURUS. After Iron Man frees him, the rogue Dio arrives. As Iron Man battles with his own creation, he wonders who the pilot in the armor is.
Dr. Tanaka informs Tony that a mysterious epidemic has broken out near the Arc Station. The rampant disease seems unstoppable, and Tony initiates his own investigation into the cause. Meanwhile, the Self Defense Forces reconnaissance satellites are acting up, and Nagato Sakurai visits Iron Man to ask for his help. Stark and Sakurai join forces, when they discover the Zodiac Mech Aquarius may be behind both incidents.
When the Arc Station has a series of malfunctions, Tony and Dr. Tanaka discover that a Zodiac computer virus has infected the Station's operating systems. The virus spreads to the city's ATM banking computers, train navigation computers and traffic controls, causing chaos. Tony decides the only way to combat the virus is to draw it to another computer… his Iron Man onboard computer!
Tony and Dr.Tanaka wake up on an isolated island with no idea how they got there and no hope of getting off the island. Missing his life-saving arc reactor and without his Iron Man armor, how will Tony and Chika be able to escape? And, who put them there in the first place?
Tony Stark meets a mysterious young girl with strange powers named Aki. Tony is shocked to find out that she belongs to Zodiac and needs Tony as Iron Man to protect her from Zodiac. Is Aki telling the truth? And even if she is, how can Tony trust her?
The plutonium needed to prime the Arc Station is stolen and Tony must don the Iron Man armor and fight against Dio. The two Iron Men must fight to the death, with the fate of Japan hanging in the balance.
Iron Man is dead! Dr. Chika Tanaka hears these astounding words from Yinsen's own lips. Meanwhile, the seriously wounded Tony Stark survives with the help of Nagato Sakurai and must devise a way to defeat Dio once and for all. However, what awaits the arrival of Iron Man is not only Dio, but also four Iron Man Sigma models as well. How will Tony Stark overcome the hopeless situation he finds himself in?
Held responsible for the event at the Arc Station, Tony Stark is arrested by the Japanese government. Nevertheless, while being transported, explosions rock the Diet parliament building, and suspicions that Stark is behind it are raised. Will Tony Stark be able to clear his name, and take out the real threat behind the Diet bombing?
Tony Stark learns the shocking truth behind Zodiac. Iron Man must muster all his remaining strength in order to stop the nefarious ambitions of his greatest adversary, the man behind Zodiac. However, when a familiar face enters the battlefield, will he be able to do what needs to be done?