An army of Wolverine clones invade Super Hero City forcing the real Wolverine and Reptil to get to the source with the 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 the same person. It soon turns out that Egghead is responsible for the Wolverine clones.

Thanos completes his Infinity Stone collection and the Super Hero Squad faces him in a final showdown for the fate of the universe. However, when requesting backup from one of their own, they encounter a betrayal that changes everything.