Silver Surfer is having a difficult time trying to fit in on Earth and chooses to leave the squad. Things get complicated when Dr. Doom kidnaps him.

A new villain named Scorpio shows up in superhero city. Nicky Fury disguises himself as a villain to infiltrate Doom's Headquarters to stop Dr. Doom from using a fractal to control a black hole.

When M.O.D.O.K. gains the power of an Infinity Fractal, he robs Dr. Doom of his powers and takes over as leader. Loki learns of this and decides to ally himself with M.O.D.O.K., forcing Dr. Doom to join forces with the Super Hero Squad in order to defeat M.O.D.O.K. and reclaim his rightful place as leader.

When 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. When Wolverine, Falcon, and Redwing 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 MODOK reluctantly help them when Iron Menace takes control of Abomination.

It's Captain America's birthday and all he wants to do is celebrate it with his fellow Super Hero Squad members and Nick Fury. In order to show his minions what real villainy is like, Doctor Doom thaws out the WWII villain Red Skull. Captain America isn't pleased to find his old enemy up to his old tricks while Doctor Doom isn't thrilled about Red Skull's enormous ego.

With Galactus attempting to eat the Skrull Homeworld and the Silver Surfer nowhere to be found. The Super Hero Squad must hold off the devourer while finding their ally (who is slowly being corrupted by the Infinity Sword) who turns out to have delayed Ronan the Accuser from coming to the Skrull Homeworld's aid.