M.O.D.O.K. and Loki conspire to overthrow Doctor Doom and take his place as leader of his allied villain group after M.O.D.O.K. eats one of the fractals. In order to stop M.O.D.O.K. and Loki, the Super Hero Squad and Storm must team up with Black Panther and an unlikely ally... Doctor Doom.

Baron Mordo possesses Iron Man turning him into the Iron Menace and escapes from the Dark Dimension, he plans to take over Super Hero City and Villainville. Wolverine, Falcon, Redwing and Abomination end up under Baron Mordo/Iron Man's control. Hulk, Silver Surfer, and Thor must team up with Doctor Strange and Valkyrie to form a team of Defenders and stop Baron Mordo's evil plot. Doctor Doom and M.O.D.O.K. reluctantly help them when Iron Menace takes control of Abomination.