When SpongeBob discovers Plankton had taken over the Bikini Bottom, a porthole opens and Goddard comes out right in front of him and Gary, scaring him. His screen opens and Jimmy Neutron appears on it and explains to SpongeBob that Plankton teamed up with the rest of the Nickelodeon villains, Vlad Plasmius, Professor Finbarr Calamitous and Denzel Crocker. SpongeBob then follows Goddard through the porthole to Jimmy's Lab.
After the villains were defeated and their worlds were saved, SpongeBob says Jimmy can visit him in the Bikini Bottom anytime and they become friends.
SpongeBob meet Jimmy again a couple more times in the other Nickoons games. In Nicktoons: Battle for Volcano Island, Jimmy contacts SpongeBob and the other Nicktoons a few times telling what to do. But he doesn't appear as a playable character.
In Nicktoons: Attack of the Toybots, he, Patrick and Tak find Jimmy in Calamitous' Toybot Factory and save him. He, Patrick and the rest of the Nicktoons then battle their way to fight of Calamitous' Toybot army.
In SpongeBob SquarePants featuring Nicktoons: Globs of Doom, He along with Jimmy and the rest of the Nicktoons teamed up together to stop giant orange Globs of goo from attacking their home worlds.