Tony Stark arrives in Japan with the aim of setting up the Arc Station in the first step in his World Peace Initiative. In front of all of Japan, he announces his new Iron Man model, Iron Man Dio, with himself in the pilot's seat. But during the demo, Dio crashes after a mysterious bug in the operating system.

Tony Stark is accused by Defense Minister Kuroda of trying to avoid controversy by sneaking plutonium into Japan aboard an undefended cargo ship. This ship has been attacked and the plutonium stolen, posing a grave threat. Tony dons the Iron Man armor and vows to retrieve the plutonium and clear his name.

Nanami is trying to get to the bottom of the rash of freak hurricanes that have killed two notable scientists. Her search takes her to Professor Sakamoto, and his former student, Dr. Tanaka. Sakamoto and Tanaka were once part of something called the Tesla Project, which was working to control the weather. Is the Tesla project a part of the weird weather attacking Japan, and even if they figure that out, how do they stop it? Can Iron Man defeat the weather?

Tony Stark is backing a charity racing event in order to burnish the image of Stark Industries. Meanwhile, Kawashima, a race car driver who's suffered career-threatening injuries, is won over by A.I.M./Zodiac who promise him they will heal his injuries if he takes out Tony Stark.

Dr. Tanaka informs Tony that a mysterious epidemic has broken out near the Arc Station. The rampant and deadly disease appears 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.

When the Arc Station has a series of malfunctions, Tony and Dr. Tanaka discover 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 are 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 Aki, a mysterious young girl with strange powers. Tony is shocked when the girl tells him that she belongs to Zodiac and mentions that she needs Tony, as Iron Man to protect her from Zodiac. Is Aki who she says she is? 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.