| # | Title | Original airdate |
|
| 01 | "Heads or Tails (Pilot)" | September 18, 1993 (1993-09-18) |
| Sonic and Tails race to Robotropolis in search of metal cotter pins in order to ward off an impending invasion by Robotnik's Buzzbombers. |
| 02 | "Sonic Boom" | September 25, 1993 (1993-09-25) |
| Sally follows up on a lead that suggests that her father, King Acorn, may be alive. |
| 03 | "Sonic and Sally" | October 2, 1993 (1993-10-02) |
| When the Princess is captured, Robotnik creates a robotic duplicate as a means of spying on and sabotaging the Freedom Fighters. |
| 04 | "Ultra Sonic" | October 9, 1993 (1993-10-09) |
| Sonic finds his Uncle Chuck after a failed mission in Robotropolis, kicking off an emotional roller coaster ride for him. |
| 05 | "Sonic and the Secret Scrolls" | October 16, 1993 (1993-10-16) |
| The Freedom Fighters embark on a mission to find some magical scrolls. |
| 06 | "Super Sonic" | October 23, 1993 (1993-10-23) |
| Sonic and Robotnik race each other in a bid to steal a dormant wizard's archive of magic spells. |
| 07 | "Sonic Racer" | October 30, 1993 (1993-10-30) |
| Robotnik holds a race in Robotropolis in a bid to lure Sonic into a trap. |
| 08 | "Harmonic Sonic" | November 6, 1993 (1993-11-06) |
| Robotnik launches a spy satellite in an effort to locate Knothole Village, the Freedom Fighters' hidden base. |
| 09 | "Hooked on Sonics" | November 13, 1993 (1993-11-13) |
| Antoine goes after Robotnik himself in a bid to impress Sally and earn personal glory. Will he succeed or fail? |
| 10 | "Sonic's Nightmare" | November 20, 1993 (1993-11-20) |
| Sonic must conquer a recurring nightmare personifying his own personal fears if he is to rescue his friends. |
| 11 | "Warp Sonic" | November 27, 1993 (1993-11-27) |
| The Freedom Fighters find themselves defending an underground city of Mobian refugees... all the while coming to terms with their own personal relationships. |
| 12 | "Sub-Sonic" | December 4, 1993 (1993-12-04) |
| In search of magical water that causes plants to grow at an accelerated speed, the Freedom Fighters journey underground where they begin disappearing one by one. |
| 13 | "Sonic Past Cool" | December 11, 1993 (1993-12-11) |
| The Freedom Fighters help a dinosaur-like species navigate through the Great Jungle while fighting off the advances of Robotnik. |
| # | Title | Original airdate |
|
| 14 | "Game Guy" | September 10, 1994 (1994-09-10) |
| Sonic is lured into a trap by someone who may or may not belong to another cell of Freedom Fighters. |
| 15 | "Sonic Conversion" | September 17, 1994 (1994-09-17) |
| Knothole's De-roboticizer is a success and Bunnie and Uncle Chuck are back to their normal selves. But is the Freedom Fighters' latest accomplishment too good to be true? |
| 16 | "No Brainer" | September 24, 1994 (1994-09-24) |
| Sonic is brainwashed by his enemies during a rescue attempt in Robotropolis. |
| 17 | "Blast to the Past (Part 1)" | October 1, 1994 (1994-10-01) |
| Sonic and Sally travel to Mobotropolis Kingdom's past, prior to Robotnik's takeover. They hope to bring an end to the invasion before it begins, and later learn the shocking truth behind the Roboticizer. |
| 18 | "Blast to the Past (Part 2)" | October 8, 1994 (1994-10-08) |
| The mission to stop Robotnik's invasion fails, and now Sonic and Sally must save their younger selves, or else cease to exist. |
| 19 | "Fed Up with Antoine/Ghost Busted" | October 15, 1994 (1994-10-15) |
| Pair of 15-minute episodes. 1)Antoine is appointed king of a biker gang, unaware of their "cannibalistic" tradition. 2)Later, Sonic and Tails investigate a possible ghost problem while camping out. |
| 20 | "Dulcy" | October 22, 1994 (1994-10-22) |
| Dulcy is summoned to the dragon mating ground as Robotnik seeks to Roboticize the remainder of her species. |
| 21 | "The Void" | October 29, 1994 (1994-10-29) |
| The Freedom Fighters find some unexpected surprises in the dimensional vortex known only as the Void. |
| 22 | "The Odd Couple/Ro-Becca" | November 5, 1994 (1994-11-05) |
| Pair of 15 minute episodes focusing on Antoine. The first one is about Antoine sharing his hut with Sonic and the second about a lovesick robot. |
| 23 | "Cry of the Wolf" | November 12, 1994 (1994-11-12) |
| Sonic and company finally make contact with another Royal Freedom Fighter group. |
| 24 | "Drood Henge" | November 19, 1994 (1994-11-19) |
| Sonic and Tails team up in order to thwart Robotnik's scheme to find the magical Deep Power Stones. |
| 25 | "Spyhog" | November 26, 1994 (1994-11-26) |
| Uncle Chuck finds himself increasingly at risk operating as a spy in Robotropolis. |
| 26 | "The Doomsday Project" | December 3, 1994 (1994-12-03) |
| Series finale. Robotnik begins the Doomsday Project a week sooner than anticipated, and now the Freedom Fighter groups of Mobius face off against the tyrant's forces in what may be the final battle. The ending leads to a cliffhanger that involves Snively and a mysterious red-eyed character (later revealed by the show creators to be Ixis Naugus). |
