Sonic and The Freedom Fighters journey to Robotnik's underground air base in a mission to reprogram the launch data on Robotnik's fleet of Stealth-Bot aircraft. While attempting to reprogram the Stealth-Bot computer system, Sally receives a computerized message she believes is from her father, indicating that he may be located somewhere within the Dark Swamp.

During a mission to one of Robotnik's factories, Sally is taken prisoner by Robotnik and Snively, who construct a roboti-sized "Sally" clone, complete with Sally's personality, and mannerisms. The double tricks Sonic into rescuing "Sally," whose tracking devise enables Robotnik to monitor the Hedgehog's every move.

Sonic and the Freedom Fighters journey to Robotnik's lab in hopes of deciphering his roboti-sizer system. While underground, Sonic spots his now roboti-sized Uncle Chuck aboard a Badlands bound mine-train and devises a plan for his rescue. The Fighters board a jet-powered railcar, dodging Hover-Units and Swat-Bots, before reaching Uncle Chuck and whisking him off into an abandoned tunnel.

Sally, Rotor, Bunnie and Antoine take off in a homemade airplane, bound for an ancient city hidden deep in the Great Mountains, while Sonic follows via his favorite transportation -- his sneakers. Their quest is the "secret scrolls" that have great powers they hope to use in their struggle with Robotnik.

While on a mission to the big city to replace Nicole's malfunctioning microchip, Sonic and Sally encounter the Guardian, a mysterious cloaked figure who guards a dormant wizard named Lazar and his computer of evil spells. Both Robotnik and Sonic believe the spells could be useful and set out to elude the watchful Guardian and steal Lazar's computer.

Sonic is hired into an obvious trap when a frustrated Robotnik decides to appeal to the Hedgehog's ego and announces a "race to determine the fastest on Mobius". Sonic decides to join the race despite Sally's objections that she needs him on a mission to take out Robotnik's power generators.

Sonic conquers Robotnik's latest evil - a vehicle designated to locate and destroy living tissue matter - during a solo mission to the Badlands. Upon Sonic's return, the Freedom Fighters honor him with a victory party. Envious of the attention Sonic's getting, especially from Sally, Antoine sets out on his own solo mission to prove his worth by capturing Robotnik.

When Robotnik launches a spy-orb that will uncover the Freedom Fighter's Knothole location, Sonic and Robot launch themselves up to the orbiting spy-sphere aboard a home-made rocket powered by Robotnik's discarded booster engine that fell in the Great Forest. Once on the heavily guarded sphere, Sonic and Robot must find the spy sensors before they locate Knothole.

When Sally uncovers Robotnik's plan to seed the cloud with toxic rain, they attempt a daring mission to sabotage the dirigible-like craft being transported by land vehicles. Mission fails when Sally, Bunnie and Antoine are captured and taken to an oil refinery island in the Great River.

When Sonic and The Freedom Fighters take out Robotnik's main computer, they're trapped by Swat-Bots in an underground tunnel, only to be rescued by a handsome teenager named Griff. Griff takes them deep beneath the Big City, where Sonic has to fight off some Rat-Bots.

Robotnik severely upsets the ecosystem above and below the surface, when he sends explosive, Robotnik snake probes drilling deep under ground in search of oil lakes. After being swept into an underground world by a whirlpool, Sonic, Sally, Antoine and Robot discover a strange creature who claims he is the last of a people who have been destroyed by surface creatures.

Tails brings a new friend home to Knothole - a baby Terra-Pod who has strayed from the herd that is currently migrating. Sonic, Sally, and some of the other Freedom Fighters return the Baby-T to its mom and the rest of the herd as they pass by Knothole on their migration run. However, Sally realizes that the herd is going in the wrong direction. Something is wrong.

Sonic reluctantly takes Tails with him to the Big City to find some cotter pins for the Freedom Fighters catapults. While in the City, Sonic is nearly eaten alive by his old dog Muttski, now a roboti-sized guard dog in the Junk Heaps. Later, while escaping some Swat-Bots, Sonic and Tails overhear Robotnik explaining his plan to defoliate the Great Forest with a chemical spray and reveal Knothole.