Magneto is working with Doom to rob all the Infinity Fractals from the Vault. His sinister plan involves letting his children, Quicksilver and the Scarlet Witch befriend the SHS to get the entry codes.
Team Toxic (Paste Pot Pete, Pyro and Zzaxx) has built a giant super spinner machine on the North Pole that can spin the Earth really fast. But it's destruction causes the polar ice caps to meld, flooding Super Hero City. Now the Super Hero Squad seeks help from Ice-Man as well as the Lethal Legion to dry up the Earth.
Doom conquers Chthon's dimension where his mother has been held captive. Once freed however, 'Coco' Von Doom proves to be anything but grateful. Meanwhile Chthon asks the Super Hero Squad to help him get his realm back and Odin orders Thor to return to Asgard and leave Earth behind.
Stardust arrives on Earth to announce the coming of Galactus, devourer of worlds. Captain America and Ms. Marvel begin constructing a space ark to save the inhabitants of Earth while the SHS team up with the Fantastic Four to face Galactus.
Galactus is about to devour Earth and not even the combined power of all the Super Heroes (and even some villains) can stop him. Iron Man decides to gather all the Infinity Fractals and reforge the Infinity Sword.
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.