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.
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.
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.
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.
Santa Claus has made an announcement - he is retiring and has picked the perfect successor - "Robotnikclaus"! Sonic and his sister resolve to persuade Santa to return and set Christmas straight. When the two track down the Santa who made the announcement, they discover he is just a phony robot and the real Santa Claus is being held prisoner.
Brandon Quark, an evil half-man, half-duck genius challenges, then teams up with Robotnik to capture Sonic. But Sonic knows their weakness, and pits the Badnik geniuses against one another, and sets himself free.
Robotnik pretends to retire, and lures Sonic and Tails into a phony vacation resort, laden with booby-traps set by Scratch and Grounder. But Sonic takes the bungee jumping, hang gliding, and skydiving in stride, and gives the bashes the bots.
When a Rebel Base is threatened by Robotnik, Sonic and Tails team up with Big Mike and Da Bears to run a booby-trapped gauntlet in their gigantic Road Warrior-like truck.
When S and G rocket to outerspace to mine a radioactive mineral from asteroids, Sonic and Tails stow away. Through a blunder by the robots, all are stranded in space, and Robotnik tries to blow all of them out of the stars.
Robotnik captures a Kangaroo named MacHopper, and uses his "brain-wipe-reprogramming-computer" to transform him into a resourceful demolitions expert (Ala MacGiver).
Robotnik invents an electron altering generator which makes Scratch and Grounder twice as fast as Sonic. When they lose it and Tails picks it up, Tails speeds through the Mobius countryside leaving disasters and accidents in his wake.
Robotnik plans to block out the sun and extinguish all life and nature on the planet Mobius. Then he creates a robot son and tries to train him in the ways of wickedness.
Robotnik invents a Brain Evolution Achievement Negatizer, or B.E.A.N., in order to make all of Mobius stupid. But instead of turning Sonic and Tails into dummies, the BEAN device turns them into three year old babies!
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.
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".
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.
Antoine decides to study martial arts but after he wrecks most of Knothole Sonic sends him off to practice in the woods. //Tails begins his training to become a real Freedom Fighter by learning tracking skills while on a camping trip.
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.
Brandon Quark, an evil half-man, half-duck genius challenges, then teams up with Robotnik to capture Sonic. But Sonic knows their weakness, and pits the Badnik geniuses against one another, and sets himself free.
Robotnik pretends to retire, and lures Sonic and Tails into a phony vacation resort, laden with booby-traps set by Scratch and Grounder. But Sonic takes the bungee jumping, hang gliding, and skydiving in stride, and gives the bashes the bots.