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.
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.
Momma escapes again from the Mobius Home for Really Bizarre People, disowns Robotnik for failing to capture Sonic, then with the help of an obscure Mobius law, adopts Sonic!
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!
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.
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.
Robotnik has his eyes set upon Queen Aleena's crown jewel, but Sonic, Manic and Sonia plan to retrieve the gem before Robotnik.
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.
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.