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.

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.

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 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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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, 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, 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.

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.

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.

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!

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.