In Robotropolis, Sonic encounters his roboticized pet dog, Muttski. Meanwhile, the Freedom Fighters have to defend the Great Forest from Buzzbombers.
While raiding a Robotropolis plant, Sally picks up a message coming from the Dark Swamp, which leads her and Antione on a search to find her father. Meanwhile, Sonic races to save them and a captured friend.
Sally gets caught by SWATbots in Robotropolis. When Sonic attempts a rescue, he actually brings back a robot duplicate of Sally created by Robotnik. Only Tails suspects something is wrong, but no one believes him.
The Freedom Fighters stumble upon a train bound for a crystal mine and Sonic finds his roboticized Uncle Chuck to be onboard. Sonic uses a power ring to temporarily restore Uncle Chuck's free will and he explains that Robotnik is after a powerful crystal, which will destroy the eco-system if taken out.
The Freedom Fighters travel to a mountain city named Maga to find the Secret Scrolls. To get them, they need to get past several tests as well as Robotnik, Snively and SWATbots.
Nicole needs to be repaired and the only place to get the needed parts is Robotropolis. There, Sally enters the Forbidden Zone and discovers a wizard named Lazar. Robotnik steals his spells and awakens Lazar, who thinks Sonic is the real thief. Sonic says he will get the spells back, but he'll have to do it without his speed.
Robotnik and Snively announce a race to be held in Robotropolis. Sonic can't help himself and enters the race, where he has to face a robot cat built to be faster than him.
Robotnik has activated the Skyspy satellite to find Knothole. Sonic and Rotor work to take out the Skyspy before it's too late.
Antoine becomes jealous of Sonic and wants to impress Sally. He comes to the conclusion that the only to do that is to capture Robotnik.
Sonic is having nightmares where Sally is roboticized. Meanwhile, Sally, Bunnie and Antoine go on a mission to stop Robotnik from creating acid rain clouds. When they're captured, Sonic has to conquer his fears to save them.
Sonic, Sally and Antoine are about to be captured when a goat named Griff saves them and takes them to an underground city named Lower Mobius. Unknown to the Freedom Fighters, Lower Mobius has a failing power source so Griff plots to steal the power stone.
Robotnik, drilling for oil, stumbles upon a super growth water and wakes a karken monster. This causes the forest to be dying and the kraken kidnaps Sonic, Sally and Antoine, leaving Rotor to save the day.
Tails finds a lost baby terrapod in the forest. The Freedom Fighters try to return the baby and protect it's herd from Robotnik.
The Freedom Fighters save a ram named Ari, who says his team is being held by Robotnik. Ari, however, has made a deal with Robotnik and gets Sonic captured.
The Freedom Fighters test a deroboticizer on Bunnie. When it succeeds, Sonic decides it's time to save his Uncle Chuck.
A ray makes Sonic lose his memory and Snively tricks him into thinking the Freedom Fighters are evil. Snively tells Sonic to locate Knothole so he can invade.
Sonic wishes Robotnik was stopped before he took over and Dulcy suggests they use the Time Stones on the Floating Island to do just that. After a series of tests, Sonic and Sally use the stones to travel back to one day before Robotnik's takeover. But will they succeed?
Sonic and Sally have failed to stop Robotnik from transforming Mobotropolis into Robotropolis. Now they have to save their past selves and friends from the roboticizer as well as the future location of Knothole.
Fed Up with Antoine: Antoine becomes king of the Nasty Hyenas, but is unaware they're going to eat him. Ghost Busted: Sonic, Tails and Antoine go on a campout. At night, Tails finds Antoine is gone and thinks a monster is nearby.
When Dulcy leaves Knothole without a word, Sonic and Sally discover she's going to Dragonsnest. Robotnik has found Dragonsnest too and plans to capture and roboticize all the dragons.
In the Great Unknown, Sonic barely escapes a vortex and brings a strange power ring back to Knothole. The ring transports Sally and Bunnie into the Void, while Sonic has gone to see Uncle Chuck and learns about Robotnik's ultimate plan.
The Odd Couple: When Sonic's hut is destroyed in a freak accident, Sonic and Antoine are forced to become roommates. Ro-Becca: Antoine accidentally activates Rotor's robot, which gets a crush on Antoine.
Sonic, Sally, Antoine and Dulcy search for the Wolf Pack to set up an alliance. Meanwhile, work on Robotnik's secret Doomsday project continues.
Robotnik seeks the Drood Henge scrolls, which give the location of the two powerful Deep Power Stones. Uncle Chuck warns Sally about it and Sonic and Tails find Robotnik already has one of the stones. The Freedom Fighters now have to find the second one before it's too late.
Robotnik suspects the Freedom Fighters have a spy somewhere in Robotropolis and discovers it's Uncle Chuck. Antoine gets captured trying to warn him and it's up to Sonic to save the day.
Robotnik releases the Doomsday pods all over Mobius. With the entire planet in danger, all the Freedom Fighters everywhere come together and Sonic prepares for the final battle.
