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.
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.
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.
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!