Strange meteors start to land on Earth. Mojo Jojo takes notice and brings his monkey army to investigate. The meteors release small monsters that attack the KND treehouse and Foster's Home for Imaginary Friends. The treehouse is overrun, but Numbuh 2 and Numbuh 5 are saved by Blossom and Bubbles (Buttercup has recently gone missing). They are then saved by Dexter and Ben.
Later, the heroes all meet to coordinate their defensive strategy. Dexter and the Professor tell the others they can build the Electro-Pulse Cannon. Dexter says the only way they can accomplish this is if they team up. The others are reluctant, but Mac is able to convince them. However, the two final components needed are in Mojo's volcano and Mandark's fortress.
Blossom, Bubbles, Numbuh 2 and Ben go to Mojo's volcano. They encounter the alien monsters, but escape with the part they need. Meanwhile, Numbuh 5 leads Mac, Bloo, and Dexter's sister Dee-Dee to Mandark's fortress. He doesn't want to give them the part, but is easily persuaded through his infatuation with Dee Dee. However, he says he'll only give them the part if he's allowed to go with them.
Dexter is reluctant to side with Mandark, but realizes he must to save the world. While the EPC is powering up, their base is attacked by the alien monsters. The heroes fight back. They destroy the alien pod, but not before it fires a blast into space. Believing they've won, the heroes celebrate. However, a badly beaten Mojo lands near them. A large composite planet appears in the sky. Mojo explains that the blast was a beacon and Planet Fusion has arrived.