The Anti-Team Nefarious Freedom Fighters are a group of heroes that are composed entirely of enemies of the members of Team Nefarious. They had formed some time after SpongeBob and Friends meet The Thief and The Cobbler. They have been of great aid ever since Ratchet and Clank aided them on that adventure, and formed an alliance consisting of Team Nefarious' various arch-enemies.
- Ratchet and Clank- Doctor Nefarious' archenemies. Ratchet is the last Lombax living in his universe when the rest were chased to another dimension and Clank is his diminutive but very intelligent robot friend and partner.
- Talwyn Apogee- A Markazian from the Polaris Galaxy and Ratchet's girlfriend.
- Cronk and Zephyr (Deceased, then revived)- Talwyn's two surrogate warbot fathers since her father's death, dying in Into the Nexus and being resurrected in the Chronicles series.
- Team Lightyear- Emperor Zurg's archenemies in Star Command who consist of Buzz Lightyear, Mira Nova, XR, and Booster.
- Major Monogram- The head of OWCA (Organization Without a Cool Acronym) consisting of semi-sentient pet animals undercover as secret agents and each with a particular archnemesis.
- Agent P- A platypus and archenemy of Doofenschmirtz, pet of Phineas and Ferb, who wears an agent fedora and fights Doofenschmirtz on a daily basis stopping his random plans while being obligated to keep his cover as a secret agent from his family.
- Kirby- A little baby malleable Nintendo iconic character who is of the Star Warriors and a frenemy of King Dedede.
- Meta Knight- A Star Warrior of the same race as Kirby and Kirby's mentor.
- Spliced Gang- A team of mutants and archenemies of Smarty-Smarts consisting of Peri, Entrée, Patricia, Two-Legs Joe, Princess Pony Apehands, Compuhorse, and Fuzzy Snuggums.
- Captain Qwark- Doctor Nefarious' original archenemy, celebrity superhero of the Solana Galaxy, former president of the Polaris Galaxy, and a fraudulent antihero.
- Melody- The young daughter of Ariel and chronic aid for the Anti-Team Nefarious Freedom Fighters because of Morgana's membership in Team Nefarious.