Set a few days after the finale of the second season, Snively achieves to take over the Robotnik Empire and gains the help of Naugus as Sonic continues his quest to free Mobius from their hands as they now count with the help of two new Freedom Fighters members.
- Sonic the Hedgehog (voiced by Jaleel White) - a free-spirited blue hedgehog with superhuman speed who TBD.
- Miles "Tails" Prower (voiced by Bradley Pierce) - a rather young twin-tailed fox who joins the Freedom Fighters to TBD.
- Knuckles the Echidna (voiced by Christopher Daniel Barnes) - a tough echidna and the Guardian of the Master Emerald who originally antagonized Sonic and later becomes one his closest allies after discovering he was tricked by Naugus to fight him.
- Princess Sally Acorn (voiced by Kath Soucie) - a beautiful female chipmunk and the heir to the Mobian throne who leads the Freedom Fighters and continues her quest to free Mobius from any kind of menace.
- Nicole the Holo-Lynx (also voiced by Kath Soucie) - an artificial intelligence who is revealed to be an intelligent but naïve young lynx and eventually joins the team, somehow developing TBD.
- Amy Rose (voiced by Elizabeth Daily) - a kinda girly female pink hedgehog who joins the Freedom Fighters who, like Sally, has a crush on Sonic and uses a giant hammer to fight anyone who tries to take down the Freedom Fighters.
- Antoine D'Coolette (voiced by Rob Paulsen) - a TBD French-accented coyote who TBD.
- Bunnie Rabbot (voiced by Christine Cavanaugh) - a skilled Southern-accented partially roboticized female rabbit who is skilled in martial arts and TBD.
- Rotor the Walrus (voiced by Cam Brainard) - a genius walrus and the Freedom Fighters' mechanic who TBD.
- Sir Charles "Chuck" the Hedgehog (voiced by William Windom) - a brilliant scientist and Sonic's caring uncle who TBD.
- Dulcy the Dragon (voiced by Cree Summer) - a ditzy female dragon who has the unique ability to create both fire and ice and TBD.
- Lupe the Wolf (voiced by Shari Belafonte) - TBD
- King Acorn (voiced by Tim Curry) - TBD
- Snively Robotnik (voiced by Charlie Adler) - Dr. Robotnik's formerly cowardly nephew who turned against him and now rules its empire in order to become TBD.
- Ixis Naugus (voiced by Michael Bell) - a mysterious creature who recently reached an alliance with Snively to conquer Mobius and take down TBD.
- Metal Sonic (voiced by Tony Jay) - a robotic doppelgänger of Sonic who is obsessed with being the one and only Sonic and tries to replace him in order to become the best Sonic.
- Anti-Sonic the Hedgehog (also voiced by Jaleel White) - an evil doppelgänger of Sonic who is out to TBD.
- Fang the Sniper (voiced by Dan Castellaneta) - a sly bounty hunter who TBD.
- Dr. Ivo Robotnik (voiced by Jim Cummings) - the former tyrannical leader of the Robotnik Empire who has been overthrown by Snively and sent into the Void, appearing mainly through flashbacks.
- New Dawn - A few days after Robotnik's imprisonment, Sonic and Sally discover that Snively has allied himself with Naugus to TBD.
- Due to its cancellation by ABC, the series moved to Fox for its third season.
- This season introduces characters recently introduced in the video games like Knuckles the Echidna, Amy Rose, Metal Sonic and Fang the Sniper.
- Tails' traits are slighty modified as he becomes more competent and starts developing his genius intellect, becoming closer to his video game counterpart.
- Nicole's origins are developed further as she was once a young lynx who got captured by Dr. Robotnik and nearly killed, resulting in her soul's transfer into a mini-computer in order to take advantage of her large intellect. She later gains her physical form after ransacking some TBD and TBD.
- Her physical from would appear in the comics as well.
- Antoine's surname is changed into D'Coolette as his jerkish characteristics are toned down and he becomes more brave and helpful rather than being an arrogant and narcissistic coward, starting to turn his affections to Bunnie as well.
- Those changes were made to make him less of a negative French stereotype and this would continue in the comics as well.
- Dr. Robotnik's first name was changed into Ivo to match his video game counterpart.