With supernatural wackiness plaguing the city, the Super Hero Squad enlists the help of the Sorcerer Supreme of the Earth dimension, Doctor Strange. However, the good doctor seems to be "off his rocker," babbling incoherently and summoning the Dread Dormammu to Super Hero City.

After helping the Super Hero Squad in a battle against Screaming Mimi, Abomination and M.O.D.O.K., Black Widow joins the team. However, unknown to them, she is actually Mystique in disguise sent by Dr. Doom to steal the Infinity Fractals from the Vault.

Enchantress places a love spell on Odin in an attempt to become queen of Asgard, but a forgotten rule forces him from the throne and makes his son Thor king instead, which both she and Loki try to take advantage of. Meanwhile, Magneto and Quicksilver discover Wanda joining with the Super Hero Squad and hitch a ride to try and take her back from them.

Ms. Marvel leads the Squaddies on a mission to rescue her namesake Captain Marvel from the Dark Surfer. But when the fight traps the Squaddies in the Soul Stone, it’s Captain Marvel who performs the ultimate sacrifice.