SpongeBob and Squidward's usual walk to work is disrupted when huge orange asteroids start raining down on Bikini Bottom. A chunk of goo falls on Squidward, causing him to be brainwashed by an alien creature called a Morphoid. He chases SpongeBob and Patrick like a zombie until Jimmy Neutron intervenes and takes them to the Mawgu Lair on Volcano Island. There they meet Danny Phantom, Tak, and a newly formed Evil Syndicate composed of Technus, Beautiful Gorgeous, Tlaloc, and Plankton. Zim and Dib arrive, with Zim joining the heroes because he is "curious", and Dib joining the Syndicate to not be on Zim's side. They make a plan to stop the Morphoid invasion, and the Wise Old Crab arrives to inform them about some technology in the lair. Jimmy uses the technology to equip everyone with weapons fitting their personality.
The group teleports to Bikini Bottom to free Gary, Squidward, and Patrick from the goo, battle an army of Morphoids, and defeat Bubble Bass, who grows gigantic and brainwashed after eating a goo-covered Krabby Patty. After being defeated, Bubble Bass vomits a large amount of goo onto SpongeBob, which leads to him intermittently speaking in an evil voice after returning to the lair. The Wise Old Crab informs them that a giant robot-like spacecraft called the Vessel of Portentia is hidden in the Mawgu Lair, and requires four special components to power it up. They then warp to Earth within Zim's universe, where GIR is playing with the first component of the vessel, becomes corrupted by the goo, and runs off. The group free Ms. Bitters, Gaz, and Professor Membrane, battle GIR at Zim's house to retrieve the component, and more goo falls onto SpongeBob. After returning to the lair, the group discover that the absorption of goo in SpongeBob's body has created a wavelength enabling the leader of the Morphoids to talk through him.