During a chaotic battle with Klaw & Screaming Mimi, a fractal's cosmic power turns the Hulk into the Gray Hulk.

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.

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 MODOK and Abomination botched up another fractal retrieval mission, Doctor Doom pairs them up with Egghead in infiltrate the Helicarrier in micro-size. When Ant-Man is called in to help, it is a micro-sized, all-out battle for the fractal.

When the Skrulls start invading the city, the Super Hero Squad must team up with the Fantastic Four to stop them. Meanwhile, Thanos forms an alliance with Dr. Doom so he can steal an alien artifact from the Baxter Building.

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.

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.

The Mayor’s re-election bid goes awry when Egghead wins by a landslide (thanks to a little mass mind-control). But his reign at city hall makes life in Super Hero City a bureaucratic nightmare for heroes and villains alike. Wolverine and the Mayor are up against every hero and villain in a desperate attempt to free everyone from Egghead’s control and stop the villains’ planned invasion.

Doctor Doom sends his "Team Toxic" (consisting of Pyro, Trapster, and Zzzaz) out in a Fractal-retrieving activity at the north pole only to run afoul of Iron Man, Thor, and Wolverine. While Flatman and Reptil lecture about the polar ice caps, the world starts flooding after Trapster sets off their super-spinner machine to self-destruct. Now Iron Man must convince Iceman to help save the day.

Dr. Doom conquers Chthon's mystical dimension to free his mother Coco Von Doom. Though Doom ends up with Chthon's evil powers, he also finds himself dealing with his mother's monstrous nagging.

Galactus arrives in Super Hero City to devour the Earth! The fate of the planet hangs in the balance, but all of the city's heroes are powerless before Galactus; omnipotence.

When Captain Marvel goes missing during a peace conference between the Kree and the Skrull, Ms. Marvel forces the Super Hero Squad to come together again to get to the bottom of this, unaware that Thanos is behind this. Meanwhile, Doctor Doom plans a prison break with Wrecker and Thunderball.

Slowly going insane in prison, Doctor Doom leads an escape plan where he distracts the Super Hero Squad using a Fin Fang Foom balloon and must lead his former allies (and two new ones) to escape from the grasp of Captain America and Ms. Marvel.

Jealous of the actions of Thor on Earth, Greek god Zeus challenges Odin to a battle between the God of Thunder and his son Hercules. Reptil sneaks along to help Thor out while the Invisible Woman is forced to broadcast the god-challenge to Superhero City to raise money for the Mayor.

After stealing the Space Gem from Thanos, Nebula seizes the teliporter of the Helicarrier to get away, but sucks herself, as well as H.E.R.B.I.E. and Wolverine, into the Negative Zone where Annihilus attacks them thinking they're after his Cosmic Control Rod.

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.

An army of Wolverine clones invade Super Hero City, forcing the real Wolverine and Reptil to get to the source with help of Firestar. Outside of the other Super Hero Squad members rounding up the Wolverine clones, Reptil is unaware that his science fair partner and Firestar are one person.

Doctor Doom returns to Latveria in hopes to regroup, but discovers that his mother Coco is free from captivity, has brainwashed her captor Chthon, and has turned his castle into a day-spa trap that has ensnared the Super Hero Squad!

After being thrown into a portal by Dark Surfer, a powerless Iron Man finds himself stranded on a world of monsters. There he meets Man-Thing and Werewolf by Night and battle Dracula and a gang of mummies led by N'Kantu, the Living Mummy. Later, it is revealed that Werewolf’s girlfriend Ellen was turned into a vampire prior to their arrival. As Iron Man tries to figure out how to leave to battle Dark Surfer, the trio of monsters declare they will form the “Supernatural Hero Squad” to save innocents on their world.

After being thrown into a portal by Dark Surfer, Hulk ends up on Sakaar and he is captured by the Red King for gladiator-themed tournament games. In order to be free of the Red King's cruelness, Hulk teams up with two other gladiators named Miek and Korg.

As Mister Fantastic and Ms. Marvel make a desperate attempt to rescue the Squaddies from their extra-dimensional exile, the evil HYDRA besieges their distant Antarctic outpost.

The Super Hero Squad suffers a time mishap that transforms several of the Squaddies into toddlers! It’s up to the unaffected heroes to find a way to fix the Super Hero Toddlers before they are stuck that way forever.

As the Dark Surfer prepares to end the universe, the half-frozen Super Hero Squad mounts a last desperate attack. Ms. Marvel reveals the secret of the Infinity Gauntlet!

After being thrown into a portal by Dark Surfer, Thor befriends a Korbonite janitor named Beta Ray Bill, and must give up Mjölnir in order to prove that he has excellent fighting skills.