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.

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.

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.

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.

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!

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.

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.

When the Impossible Man’s wife kicks him out, the irrepressible funster ends up crashing with the Super Hero Squad. But to save his marriage, Impossible Man attempts to do something no one else has been able to do – defeat the Dark Surfer.

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.

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.

Thanos destroys the Nova Corp and takes Nova captive in order to get his hands on the Power Gem, leading to Iron Man and Hulk to recruit Hercules and She-Hulk to rescue him. Meanwhile, H.E.R.B.I.E. falls for Nova's messenger droid.

After being thrown into a portal by Dark Surfer, Wolverine winds up on a world populated mainly by dinosaurs and encounters the High Evolutionary who asks him to help with a particular dinosaur named Devil Dinosaur in exchange that he helps to get Wolverine back to Earth.

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.

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 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.

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.

Thanos uses the Mind Gem to control Hulk who goes on a sleepwalking rampage. The Super Hero Squad must enter the dream realm to fight back, even if they have to get help from Nightmare.

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!

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 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.

A mishap between Thanos' new Time Gem and the Scarlet Witch's hex powers sends her back to World War II, where she must assist Captain America and the Invaders stop Red Skull from launching a rocket that will destroy Europe.

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.

Thanos recruits Iron Man, Hulk and the Scarlet Witch for a match against the Squadron Supreme of another dimension in a battle of heroes for the Grandmaster's Mind Gem.