SpongeBob discovers that Plankton has deployed gigantic vacuum machines across Bikini Bottom. Before he can respond, Jimmy Neutron's robot Goddard arrives through a portal with a message: Professor Calamitous has copied Jimmy's Universe Portal Machine and formed a Syndicate with Plankton, Vlad Plasmius, and Denzel Crocker. The four villains are draining energy from multiple worlds to power a Doomsday Machine. SpongeBob joins Jimmy, Timmy Turner, and Danny Phantom to stop them — fighting through the Ghost Zone, Bikini Bottom, and Dimmsdale, freeing Danny's parents, Patrick Star, imprisoned fairies, and Mr. Krabs along the way. Eventually a spy device planted in Goddard leads the heroes to Calamitous' lair. The Syndicate is defeated, SpongeBob pulls the plug on the Doomsday Machine, and the four heroes go their separate ways.