As the celebration to mark Villain Ville being closed off from Super Hero City turns into a disaster area, Iron Man, Falcon and Wolverine do battle with the Mole Man to retrieve an Infinity Fractal. Meanwhile, Ms. Marvel leads Hulk, Thor, Silver Surfer, and Storm in battle against Mole Man's creatures, Manoo, Megataur and Tricephalous.

Dr. Doom is fed up with the Super Hero Squad constantly foiling his plans, so Enchantress decides to help by casting a love spell on Thor to make him fall in love with her. However, the love spell accidentally hits Ms. Marvel instead, causing her to fall in love with M.O.D.O.K. Meanwhile, Skurge intends to defeat Thor himself so Enchantress will love him.

Silver Surfer's past as Galactus' herald is revealed as he encounters another herald, Stardust. But Doctor Doom has plans of his own for Stardust and her big boss.

Galactus arrives in Super Hero City to devour the Earth! The fate of the planet hangs in the balance, but all of the city's heroes are powerless before Galactus; omnipotence.

When Captain Marvel goes missing during a peace conference between the Kree and the Skrull, Ms. Marvel forces the Super Hero Squad to come together again to get to the bottom of this, unaware that Thanos is behind this. Meanwhile, Doctor Doom plans a prison break with Wrecker and Thunderball.

After the Super Hero Squad gets imprisoned by the Skrulls, Falcon's trump card, in the form of Scarlet Witch, is the only hope to stop the war between the Kree and the Skrull and to defeat Thanos and his Soul Gem.