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.
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 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.
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.
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.
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'.
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.
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.