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.

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.

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

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.

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.

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!

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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, 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.