Mole Man unleashes Megataur, Tricephalous and Manoo on Superhero City while searching for a fractal buried deep beneath the ground. The Super Hero Squad tries to stop both him and his minions, but Mole Man still has Fin Fang Foom waiting in the wings.
Doctor Strange is acting weirder than usual, and magic is affecting the heroes and villains in unexpected ways. When Strange opens a portal to the Dark Dimension, the dread Dormammu enters Super Hero City and soon becomes invincible when he obtains all the recovered Infinity Fractals.
The mysterious Scorpio steals a Collider control program from Stark Industries and manages to keep one step ahead of the Super Hero Squad at all times. An impressed Doc Doom wants Scorpio, not to mention the Stark tech, to help him create a black hole.
Enchantress uses her magic to crash the Helicarrier into the Great Wall near Villainville and Ms. Marvel blames Falcon for the crash. After attempts to bunk in at Stark Industries, Punisher's van, and Reptil's house, they try the Sanctum Sanctorum where Doctor Strange warns them that there is a magic threat responsible for their misfortunes.
Wolverine wants to quit being a Squaddie and is reassigned to the All Captain Squad. As 'Captain Canada', he joins Captain America, Captain Britain, Captain Australia, Captain Brazil and Captain Liechtenstein. Their first mission pits them against Plant Man in the South American Rainforest. Meanwhile, back in Super Hero City, Doctor Doom is trying to recruit the Ringmaster into his Lethal Legion and Reptil steps up to replace Wolverine's animal factor in the SHS lineup.
Thanos approaches Doom with an unholy alliance and asks the Lethal Legion to steal an artifact from the Baxter Building. Meanwhile The Super Squad teams up with the Fantastic Four to fight off a Skrull invasion.
Shield agent Black Widow helps the Super Hero Squad out in a fight and is invited to stay aboard the Helicarrier. Little do the Squaddies realize she is actually Mystique in disguise and reporting to Doctor Doom.
War Machine teams up with Iron Man when Doctor Doom, Crimson Dynamo, and Melter band together in a plot to eliminate Iron Man. Meanwhile, Wolverine and Reptil face off against Abomination and M.O.D.O.K. in a game of golf.
Captain America sends Wolverine back to Xavier Academy to get his diploma and finish his remaining credits. Reptil tags along to see what Xavier Academy is like. To make matters worse, Ringmaster shows up and hypnotizes the entire X-Men team.