After a disastrous failed mission, Sonic laments that they can't go back and prevent Robotnik's take-over. Dulcy tells them they can and takes Sonic and Sally to the Floating Island where they find the "Time Stones", but in order to time travel to a desired destination/time, they have to synchronize their thoughts and Sonic allows his to drift (to thoughts of chili dogs).

After Antoine saves Sally's life during a raid, Sonic can't stand his bragging and zips in to see Uncle Chuck, who finds out his "bug" in Robotnik's HQ is malfunctioning.

When a blizzard hits Knothole causing Dulcy to demolish a few huts during a landing, Sonic is forced to bunk with Antoine. It is truly a marriage of opposites, with Antoine constantly picking up after Sonic. Finally, after making a complete mess of the kitchen fixing chili dogs, Sonic retires for the night. A few hours later, an exhausted Antoine follows, but almost immediately, he awakens to see Sonic "sleep-racing", leaving behind a trail of destruction. Antoine snaps and, giggling maniacally, goes on a rampage. //During a rainstorm, Rotor is putting the finishing touches on his new female robot assistant, named Ro-Becca, when he has to leave. While he's gone, Antoine accidentally activates her and it is love at first sight, for her. She chases Antoine and, after a series of mishaps, during which he catches a cold, she corners him and attempts to cure his cold with "tough love".

In Part II, Sonic and Sally steal the Roboti-sizer plans, stop the Destroyer from polluting the Great Forest and save Little Sonic, Little Sally and Dulcy's mother, Sabina, but are unable to prevent Robotnik from roboti-sizing Uncle Chuck or from relegating the King to the Void.

The Freedom Fighters, with new addition, Dulcy, develop a De-Roboti-sizer and try it out on Bunnie. It's a success and, against Sally's wishes, Sonic battles Robotnik's newest weapon - a Virtual Reality Shriek-Bot - and impulsively brings Uncle Chuck back to Knothole to de-roboti-size him. All goes well until Bunnie suddenly reverts and the De-Roboti-sizer explodes.

Sonic attempts a solo rescue to prevent prisoners from being roboti-sized and is hit by a Memory Scrambler that erases short-term memory. Snively finds Sonic and brainwashes him into believing they are friends and that the Freedom Fighters are a subversive group which he infiltrated on Snively's behalf.

The Freedom Fighters run into a Swashbuckler, named Ari, battling Swat-Bots. Sonic diverts them, allowing Ari to escape. After hearing that Robotnik is holding his band of Freedom Fighters hostage, Ari decides to help Sonic free them. But there's something about him Sally doesn't trust. Her instincts prove to be right.

When a Pod lands in Knothole, Sonic and Sally realize the Doomsday Machine is already in operation. The Freedom Fighter groups break into the Doomsday Machine, only to find Robotnik let them in. Sonic tries to destroy the control room but is thwarted and almost roboti-sized, then escapes using multiple Power Rings.

Antoine decides to study martial arts but after he wrecks most of Knothole Sonic sends him off to practice in the woods, where he runs into a scurvy band of Road Warrior-types, called the Nasty Hy… // Tails begins his training to become a real Freedom Fighter by learning tracking skills while on a camping trip with Sonic and Antoine.

After Dulcy exhibits strange behavior, Sally discovers she's going through a "rites of passage" stage of her adolescence. In Dragon tradition, she is drawn to Dragon Lair, a migratory nesting ground, through trance-like visits from her mother. Unfortunately, Robotnik, who is determined to capture all the remaining Dragons, taps into the same information. He captures a Dragon, but it isn't Dulcy.

After Sonic is almost sucked inside the Void, he finds a huge Ring which Sally believes is an ancient relic but it turns out to be trick of the Sorcerer, Nagus. Sally and Bunnie are drawn inside the Void and when Sonic comes to rescue them, Nagus pretends to be the King so Sonic will use his speed to transport him outside.

When Uncle Chuck's "bug" reveals Robotnik's search for the legendary Deep Power Stones, he informs Sally, who tries to retrieve data regarding the Royal Family Secret. But she's denied access via a time-encoded lock-out. Meanwhile, on a training mission, Sonic and Tails happen upon Snively's Drood Henge dig and Tails is captured.

On a mission to contact the first Freedom Fighters on the King's List, Sonic and the others are forced to travel through a tunnel which carries a "curse" against all intruders.