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.
Bob and the gang have got a big job on - repairing some pipework in Farmer Pickles field. / Bob, Scoop & Muck have to make repairs to a tunnel. When they arrive on site, Bob sends Muck ahead into the tunnel with a load of bricks.
Sleet and Dingo plan to collect the taxes owed to Robotnik from the Duke of Velcronia but keep it for themselves.
Sonia discovers that the watch she received from her friend is actually a monitoring device for the Robotnik Intelligence Agency.
A homecoming is interrupted for Sonic, Sonia and Manic when Sleet and Dingo arrive to collect back taxes after returning to their birthplace.
A captain of the Queen's guard is captured before he can reach the secret rendezvous where he was to meet Queen Aleena.
Robotnik announces that he will marry Queen Aleena in a plot to become the king of Mobius.
Robotnik has his eyes set upon Queen Aleena's crown jewel, but Sonic, Manic and Sonia plan to retrieve the gem before Robotnik.
Sonic becomes aggravated that maybe their efforts of fighting for freedom seem pointless. Sonia suggests that they go to the Oracle for advice.
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.
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.
Bob and the gang have got a big job on - repairing some pipework in Farmer Pickles field. / Bob, Scoop & Muck have to make repairs to a tunnel. When they arrive on site, Bob sends Muck ahead into the tunnel with a load of bricks.
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.
Sonic attempts a solo rescue to prevent prisoners from being roboti-sized and is hit by a Memory Scrambler that erases short-term memory.
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.
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".
Lazy con-man Bo Beagle has the Choas Emerald ring stuck on his finger, and Robotnik wants it for one of his evil schemes.