Their meeting place was the Junkman's ship. They appeared in the episode of the same name but, by then end of the episode, Zix, Travoltron, and Tee had quit the alliance, and the rest were trapped in the past.
- King Goobot (leader)
- Finbarr Calamitous
- Beautiful Gorgeous
- The Junkman
- Zix, Travoltron, and Tee (formerly)
- Grandma Taters
- Baby Eddie
- Eustace Strych
- The villains were supposed to return in the planned season four. One of the overarching stories would've been about them escaping from prehistory, rebuilding their organization and planning the final blow to Jimmy and his friends. In the planned series finale, all of Team Neutron would've teamed up and defeated them once and for all.
- Meldar Prime, Dr. Sydney Moist, Evil Jimmy Neutron and Bueford Lee Stormshuckle are not in the League of Villains and are therefore the only four villains that don't appear in the special.
- The League of Villains are parodies of DC Comics' Legion of Doom, Secret Society of Super Villains, Brotherhood of Evil, Injustice League, Rogues and Marvel Comics' Masters of Evil, Brotherhood of Evil Mutants, Frightful Four, Sinister Six, Sinister Syndicate, Lethal Legion, Decepticons and Predators from transformers franchise, Arachnos from city of heroes/ city of villains, Rengades from chanellenge of the gobots, Injustice Friends from dexter's laboratory, Sinister Society and Frightful Five from amalgam comics, Cyberdata from cyber force, Tyrannos from dinosaucers, V.E.N.O.M. from m.a.s.k.s., Shadaloo from street fighter and Galactic Empire from star wars.