Boy Genius Tony Stark is left the sole survivor when his father's plane crashes. Now an orphan, he is presented with a questionable 'last request' of his father: Live with the Rhodes and go to school.
Tony feels that Obadiah Stane, the new head of Stark International, is responsible for his father's death. Tony's suspicions peek when he learns that Stane is changing his dad's inventions into powerful weapons known as the Earth Movers. While investigating the situation, Iron Man confronts a mysterious person named The Mandarin.
After Tony is captured by a secret organization, he learns that Gene's father has something to do with it.
Despite Rhodey's reservations, Iron Man builds an alliance with a man named Blizzard. Wanting to take out Obadiah Stane, Tony feels that the new partnership will be beneficial. But is Blizzard all that he seems to be?
When Pepper's father is targeted by arms dealer Mister Fix, Tony must save the day without revealing his secret. However, this task becomes nearly impossible when Mister Fix sends his agent Whiplash after Pepper.
Ivan Vanko, a scientist who was thought to have been left in space two years ago, crash lands in New York City. Alive because of an environmental suit, called the Crimson Dynamo, Vanko seeks revenge on the program that put him in space in the first place- Project Pegasus. It's up to Iron Man to stop Vanko from destroying Project Pegasus.
The pressures of living a normal teenage life and being Iron Man become too much for Tony. Deciding he doesn't need school anymore, Tony quits and focuses on saving the world as Iron Man full time. But when a new villain, called the Living Laser, appears, Tony learns that he has to graduate in order to take over Stark Industries.
Tony sneaks into Stark International to catch a glimpse of the new Stealth Armor. Unfortunately, the building locks down and Tony is stuck inside. With the help of Rhodey and Pepper, Tony must find a way out of the building without revealing his secret identity.
Tony and his friends' search for the ancient Makluan Rings goes awry when the guardians of the Rings, the Dreadknights, arrive.
During the school science fair, Tony is approached by the leaders of an organization known as the Advanced Idea Mechanics. Offering up his help, Tony inadvertantly creates a new enemy, the Controller. With Tony's friends under its control, Iron Man must step in and save the day.