With all of Villainville in jail, the Super Hero Squad is about to disband. Just then Captain Marvel disappears on his way to a peace mission, leading to hostility between the Kree and Skrull empires.
The Super Hero Squad has been captured by the Skrulls. But Falcon reveals they have a stowaway on the S.H.I.E.L.D. Helicarrier, namely the Scarlet Witch.
Thanos acquires the Time Gem and attempts to send the Super Hero Squad back a billion years in the past. But Scarlet Witch uses her hex power to avert the time beam, only to end up in World War Two all by herself.
Tired of having to suffer Captain America's therapy sessions, Doctor Doom plans a prison break. Phase one is getting the Super Hero Squad out of the way by organizing a wild Fin Fang Foom chase.
Zeus challenges Odin to a contest of champions between their favorite offspring, Hercules and Thor. The Mayor wants to broadcast this event on TV and gets the Invisible Woman to slip into Asgard unnoticed with a video camera.
Thanos challenges the Grandmaster for the Mindstone. They pit three Squaddies (Iron Man, Hulk & Scarlet Witch) vs the Squadron Supreme (Nighthawk, Hyperion & Power Princess).
Thanos has the Space Gem stolen from him by his older sister Nebula. She uses the Squad Helicarrier's Teleporter to escape, but ends up in the Negative Zone. Wolverine and H.E.R.B.I.E. team up as they were the only ones aboard the Helicarrier at the time. Having just returned from a trip to Six Eggs Over Easy amusement park, Iron Man & Falcon venture into the Zone to save them.
Galactus is about to devour the Skrull Homeworld because the Silver Surfer is too busy fooling around with the Infinity Sword. The Squadies delay the Hulk's bath and head off into space.
Enchantress puts a spell on Odin to make him marry her but since she has no royal blood, Thor has to take his fathers place as ruler of Asgard. Meanwhile Magneto and Quicksilver are looking for the Scarlet Witch and assume she is being held captive by the Super Hero Squad.
Thanos is destroying the Nova Corps to capture the Power Gem. Iron Man enlists Hercules and She-Hulk for extra strength factor to face off in outers space.
Super Hero City is invaded by free roaming Wolverines. The original Logan smells out that Egghead is behind the creation of his clones. He teams up with Reptil and Firestar, the former being unaware that the latter is also his science fair partner at school.
When Doc Doom returns to Latveria, he finds his mother has turned castle Doom into a luxurious spa. And the among the chilled out guest are several members of the Super Hero Squad.
As soon as Thanos has finally acquired all six Infinitiy Stones, he is immediately confronted by (in this order) Doctor Doom, the Super Hero Squad and the Silver Surfer, wielder of the Infinity Sword.
Dark Surfer has banished the Squaddies through time and space. Thor finds himself on space station Scuttlebut where janitor Beta Ray Bill is holding off the Stranger's attack. What is more, Thor agrees to do so without the help of Mjolnir.
Falcon & H.E.R.B.I.E. arrive 40 years into an alternate future where the world is governed by Sentinels, and ruled by the Scarlett Empress. They team up with the aged Magneto and the last living hero known only as 'The Man'.
Iron Man enters a world without heroes, ruled by Dracula and his mummies. He teams up with two 'good monsters': Man-Thing and Werewolf by Night, while waiting for his armor to recharge.
Wolverine lands on a dinosaur world where the High Evolutionary wants to separate MoonBoy and his tribe of Hill Folk from Devil Dinosaur and his kin. Meanwhile, the Mayor faces off against the Dark Surfer.
Scarlet Witch ends up in the Marvel 1602 universe where she helps the inhabitants of Super Hero Town face Captain Doom and his pirates. Afterwards, she is tried for witchcraft.
Cap, Ms Marvel & Mr. Fantastic travel to the Savage Land in an attempt to return the Squaddies from all the different dimensions they have been exiled to. But Baron Strucker and Hydra are also there, seeking a way to escape from Earth.
Impossible Man has been kicked out by his wife, so he asks to stay in the Squaddies Helicarrier. But then he gets the idea to take over the Universe from Dark Surfer to impress the Impossible Woman.
Ms. Marvel instructs the Squaddies to help Captain Marvel fight the Dark Surfer, but she, Thor and Iron Man end up in the Soul Stone with Thanos and Warlock.
Thanks to the wisdom of Warlock, the Super Hero Squad has figured out that each one of them can use their specific Strength Factor to counter one of the Infinity Stones.
