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.
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.
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.
Sonic, Manic and Sonia find an abandoned baby in an alley and begin to look for the baby's parents. Manic becomes very fond of the child.
Sonic becomes aggravated that maybe their efforts of fighting for freedom seem pointless. Sonia suggests that they go to the Oracle for advice.
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.
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.
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
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".
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.
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.
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.
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.
Robotnik installs a new "obedience microchip" in Scratch and Grounder and orders them to drill for a rare mineral in a tropical mountain. With his Freezomatic machine, Robotnik covers the mountain in ice and runs a Hermit out of his home.
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).