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.
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.
After the Super Hero Squad gets imprisoned by the Skrulls, Falcon's trump card, in the form of Scarlet Witch, is the only hope to stop the war between the Kree and the Skrull and to defeat Thanos and his Soul Gem.
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.
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.
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.
With Galactus attempting to eat the Skrull Homeworld and the Silver Surfer nowhere to be found. The Super Hero Squad must hold off the devourer while finding their ally (who is slowly being corrupted by the Infinity Sword) who turns out to have delayed Ronan the Accuser from coming to the Skrull Homeworld's aid.
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.
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.
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.
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.
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!
As Thanos gets all the Infinity Stones, the Squaddies face betrayal at the hands of one of their own! In this mind-shattering climax to the Infinity Gauntlet Saga, the very fate of the universe hangs in the balance.
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.
After being thrown into a portal by Dark Surfer, Falcon and H.E.R.B.I.E. find themselves in an alternate reality where Scarlet Witch is an evil emperor who rules the world. With help from an elderly Magneto and a strong Reptil, Falcon and H.E.R.B.I.E. try to convince Scarlet Witch that she is good and let the world be in peace.
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, 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.
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.
After being thrown into a portal by Dark Surfer, Scarlet Witch ends up in the Marvel 1602 universe where she finds a town under attack by pirate versions of Doctor Doom, MODOK, and Abomination. Unfortunately for Scarlet Witch, the townspeople do not appreciate witches.
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.
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.
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.
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.
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!
The Six Squaddies must each face the Dark Surfer one on one, in a final battle for the fate of destiny for the fate of reality that takes them to the edge of the universe-and a last stand at the cosmic Infinity Pool!
