Prior to the beginning of the series, the villainous Doctor Doom, in pursuit of universal domination, attempts to acquire the limitless reality-bending power of the "Infinity Sword." He is stopped by Iron Man, but as a consequence of their battle, the sword is shattered into numerous fractals that rain down on Super Hero City. Doctor Doom has forged alliances with just about every supervillain forming the Lethal Legion in order to hunt down the scattered fractals, each of which possess dangerous and different powers of their own. The second season revolves around the Super Hero Squad gaining a new team member (Nova, Captain Marvel, the Squadron Supreme, Hercules, Zeus, Annihilus and She-Hulk. Thanos is the one of the main villains.
The Six Squaddies must each face the Dark Surfer one on one, in a final battle for the fate of reality that takes them to the edge of the universe-and a last stand at the cosmic Infinity Pool that brings everything full circle!
As the Dark Surfer prepares to end the universe, Ms. Marvel reveals a secret that could finally bring down the Infinity Gauntlet! Meanwhile, Doctor Doom prepares one final measure to try and stop the Dark Surfer with his own villainous team.
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.
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.
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.