As the celebration to mark Villain Ville being closed off from Super Hero City turns into a disaster area, Iron Man, Falcon and Wolverine do battle with the Mole Man to retrieve an Infinity Fractal. Meanwhile, Ms. Marvel leads Hulk, Thor, Silver Surfer, and Storm in battle against Mole Man's creatures, Manoo, Megataur and Tricephalous.

While in battle with Abomination and the Wrecking Crew, new Squaddie Reptil loses an Infinity Fractal. With both sides scrambling to retrieve it, Reptil, with Wolverine's help, learns to face his fears and what it means to be a hero. Meanwhile, Hulk inadvertently joins a mariachi band.

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.

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.

When the city is attacked, the squad investigates, only to find that a little girl named Brinny Bratten, who had a fractal stuck in her tiara, that gives her a large and terrifying power over reality. The Heroes For Hire are helping the Squad find her father, while Doom plans to use the chaos to his advantage.

Loki teams up with Doctor Doom in a plot to take over Asgard. Meanwhile, the latest Infinity Fractal causes Thor to lose his memory and it's up to Iron Man and Hulk to help him remember who he is.

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 Falcon is presumed the cause of crashing The Helicarrier, The Squad is forced to relocate. Meanwhile, Enchantress and M.O.D.O.K. plan to attack Superhero City while the squad is tired from moving from place to place.

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 he is tired of all he can take with the Super Hero Squad, Wolverine joins up with the internation All-Captains Squad (consisting of Captain America, Captain Australia, Captain Brazil, Captain Britain, and Captain Lichtenstein) as Captain Canada where he helps them fight Plantman in the Amazon. Meanwhile, the rest of the Super Hero Squad have an embarrassing encounter at Ringmaster's circus when Doctor Doom sent Abomination and MODOK to recruit Ringmaster.

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.

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.

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.

Dr. Doom is fed up with the Super Hero Squad constantly foiling his plans, so Enchantress decides to help by casting a love spell on Thor to make him fall in love with her. However, the love spell accidentally hits Ms. Marvel instead, causing her to fall in love with M.O.D.O.K. Meanwhile, Skurge intends to defeat Thor himself so Enchantress will love him.

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.

When a smilodon is brought to Super Hero City from the Savage Land, a mysterious jungle lord named Ka-Zar shows up stating that the smilodon is actually his companion Zabu. When the Super Hero Squad encounter Ka-Zar, they learn of his mission and help him rescue Zabu. Meanwhile, Doctor Doom sees the Star Quartz (which will bind and merge any metal in the presence of Vibranium) around Zabu's neck and sends Toad, Thunderball, Sabretooth, and Batroc the Leaper to steal Zabu in a plot to reforge the Infinity Sword.

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.

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.

Magneto is in town and he tricks his children Quicksilver and Scarlet Witch into helping in a sinister plot to steal the Infinity Fractals at the Vault for Doctor Doom. During the first fight, Falcon develops a crush on Scarlet Witch after she heals Redwing.

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.

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.

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.

Silver Surfer's past as Galactus' herald is revealed as he encounters another herald, Stardust. But Doctor Doom has plans of his own for Stardust and her big boss.