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?