Tony fakes his death after several attempts on his life, which seemed connected to a larger plan involving the abduction of four industrialists by the Mandarin. Tony returns in a more powerful suit of armor and has to team up with a double crossed Mandarin to stop Fin Fang Foom from taking over the world.
Jim nearly drowns in his War Machine armor, making it hard for him to put the armor back on. Iron Man, meanwhile, discovers the son of a former Stark employee is seeking revenge as Firebrand.
A.I.M. takes credit for a deadly terrorist attack, but Iron Man finds the source to be a powerful space station named the Star Well. A kind man, Arthur Dearborn, lives on the station, which is guarded by the mighty Sunturion. Iron Man tries to get Dearborn to evacuate before A.I.M. attempts a take over.
An intercepted A.I.M. signal leads Tony to find his thought dead father, Walter Stark. While he deals with painful memories, Tony also discovers what really happened to his father and why S.H.I.E.L.D. was involved.
Julia and several employees are kidnapped in Cairo, Egypt, by Tony's former lover, Madame Masque. She has dedicated herself to finding the Golden Sepulcher of Isis to cure her disfigured face. But the spirit of Isis possesses her, forcing Iron Man to fight her.
Hawkeye's spine is wounded in a battle with Ultimo. Iron Man shrinks down to molecular size to implant a chip that will save him. But no one knows is that a mysterious Hacker is in control of Ultimo and now H.O.M.E.R. too.
An unmanned alien ship arrives on Earth with a message begging for Iron Man's help against Dark Aegis. Iron Man is determined to help, since it was he that left Dark Aegis adrift in space, and readies the ship for take off. Jim, who is determined to conquer his fears, suits up as War Machine again to accompany Iron Man. But a dangerous stoaway threatens their mission.
Modok has found one of the missing rings, but the Mandarin soon reclaims it. While Iron Man uses H.O.M.E.R. to find where Modok is hiding, the Mandarin uses his rings to see what Iron Man has been doing in recent months.
One of the Mandarin's missing rings creates a time rift and Julia gets sucked in. Iron Man manages to recover the ring with Bruce Banner's help, but before Julia can be saved, The Leader steals it and now possess two of the Mandarin's rings. The Leader plans to travel back to before the gamma bomb detonation and gain the power of the Incredible Hulk.