When his industrialist father Howard Stark disappears in a plane crash after refusing to weaponize the Earth Mover at Obadiah Stane's behest, 16 year old genius Tony uses a high-tech suit of armor he has constructed and investigates a charge that Stane may have been involved in his father's death. As Iron Man, Tony spends his time stopping Stane's plans and saving the world from other villains such as Mandarin, Mr. Fix, Whiplash, A.I.M., Madame Masque, Living Laser, the Maggia, Firebrand, Controller, Crimson Dynamo, Blizzard, Killer Shrike, Unicorn, M.O.D.O.K., Ghost, Fin Fang Foom, Black Knight, and Technovore. He is assisted in his crime fighting efforts with help from James Rhodes and Pepper Potts. Now dependent on his phenomenal technology for survival, Tony must balance the pressures of teenage life with the duties of being a super hero.
Obadiah Stane hires Ghost to steal the Iron Man armor, so Ghost does a trick to make a helicopter shut down. This alerts Iron Man to save the men in the helicopter, and fly back to the Armory. As Tony goes back to the Armory, Ghost follows. Tony's identity is revealed to Ghost, and Ghost steals all of the armor specs. He sells them both to Obadiah Stane and Justin Hammer, and tells Tony he won't reveal his identity until he is 18, to blackmail him.
When Mr. Fix rematerializes the Living Laser on Justin Hammer's orders, unexpected complications split him into two separate halves. The Dark and Evil Half seeks out to destroy Iron Man and conquer the world, while the Good and Light Half tries to warn Tony and help him. After a fight with the Dark Half, Tony returns to the Armory to find the Light Half, where the Light Half asks for his help. Tony denies this, and is angry.
With Stark International on the line, Tony (who is severely ill and injured) suits up in the all-new Mark 2 Iron Man armor to defeat Whiplash, Blizzard and Mr. Fix, with the help of War Machine. As a result Iron Man and War Machine successfully defeat their foes. Meanwhile, the Mandarin awakens the 6th Ring's guardian, "The Melter". As Howard is nearly killed, the Mandarin defeats the Melter. As Howard complains about what just happened, the Mandarin brings up about never seeing Tony again.
Mr. Fix's mysterious new boss orders the abduction of 21-year-old multibillionaire Justin Hammer, so Mr. Fix releases the new and improved Whiplash 3.0 to complete this mission. It seems that Gene Khan (the Mandarin) in the last episode of season 1 said that Howard Stark (Tony's father) is alive and he is with Gene to find the 6th Makulan Ring. But when Tony Stark returns from his journey to China, he suits up to stop Whiplash. Tony successfully stops Whiplash from abducting Justin Hammer. When Whiplash returns back to base empty handed, Mr. Fix's employer is furious and now orders the abduction of Obadiah Stane...
Rhodey dons the War Machine armor and saves his friends just in time and sacrifices Zhang to Fin Fang Foom, activating the 5th rings power. However, Gene retakes the rings and starts losing control as Tony has to stop him.