The second season covers the Armor Wars saga and Stane International storylines. The first half of Season Two reflecting the Armor Wars has Tony and Rhodey as his definite partner War Machine fighting many people who have stolen Stark's armor tech and seek to exploit the stolen Iron Man specs for their own purposes. The enemies young Stark fights during this version of the Armor Wars include the Ghost who steals Iron Man specs and knows that Tony Stark is Iron Man. Ghost sells the specs to both Justin Hammer and Obadiah Stane but says he will not reveal Iron Man's true identity until Tony turns 18. Justin Hammer makes an armor with the Iron Man specs with the armor being called Titanium Man.Doctor Doom joins forces with Stane to attain the Iron Man armor operating system. Stane builds the Iron Monger armor which is revealed actually to be a direct upgrade from Crimson Dynamo armor (version 3) and is much larger than in the comic book and live action movie realities.The Armor Wars conclude as Obadiah Stane discovers the identity of Iron Man. Stane steals Iron Monger and is intent on destroying Tony once and for all.

While Tony is fighting the Armor Wars, Howard Stark is shown to be alive and forced by Gene to find the other 5 Makluan Rings. Gene continues to find and secured the sixth, seventh, eighth, and ninth rings for himself during this time. This part of the season also included Makluan Guardian versions of Melter, Sunturion, Grim Reaper, and Grey Gargoyle who guard the remaining Makluan Rings.

The second half of season two showcase the printed page storyline of loosely based on the "Stane International" story arc. Justin Hammer (instead of Obadiah Stane) successfully buys control of Stark International. Stark, Rhodey and Potts all agree to fight against Hammer and his weaponization of Stark International's projects. Unlike the printed page version, Stark and Rhodes reject the title of Circuits Maximus for the new start-up and settle on "Stark Solutions" (opposite to Stark Enterprises of the printed page).

By the end of the second season, Pepper has assumed the armored identity of Rescue.



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