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?

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?

Held responsible for the event at the Arc Station, Tony Stark is arrested by the Japanese government. But while being transported, explosions rock the Diet parliament building, and suspicions are raised that Stark is behind it. 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. But, when an familiar face enters the battlefield, will he be able to do what needs to be done?