Sonic, Sonia, and Manic are the children of Queen Aleena Hedgehog, the rightful ruler of Mobius, and are pursued relentlessly by Doctor Robotnik and his bumbling bounty hunters sidekicks, Sleet and Dingo. As infants, the siblings were separated and placed in hiding to fulfill a prophecy made by the Oracle of Delphius that the triplets would grow up to find their estranged mother, overthrow Robotnik, and take their places once more as Mobius' rightful rulers.
The Hedgehogs steal historical artifacts of Mobuis from Robotnik before he can pawn them off at an auction. Sonic and Sonia take one of the pieces to a university professor who informs them that the artifact is actually a bomb from the Mobian war. The Hedgehogs must act fast to retrieve the bomb and protect the treasure that is the key to Mobius past.
A faction of the Freedom Fighters is wiped out by a swarm of metallic fly-bots. When Manic goes in search of the insects, he is stung with serum, making him loyal to Robotnik. Sonia finds Manic communicating a radio message to Robotnik and realizes her brother is under a spell. It is up to Sonic to exterminate the metallic pests.
A speed enhancing fluid deemed Sonic Tonic is created by Robotnik to make him as fast as Sonic so that he may finally catch him. Robinik's plan is successful and Sonic is captured, yet when Dingo begins to feel the side effects of the tonic, Sonic is able to make a run for it with a vial of the tonic in tow. Unaware of the side effects of the tonic, Manic and Sonia, envious of Sonic's speed, decide to use the tonic on themselves.
The Hedgehogs converge on the Floating Island, in their latest attempt to find their Mother. Sleet and Dingo also have an interest in this island that involves the Chaos Emerald, which is the island's life-force. But, before either party can achieve their goals, they have to get through Knuckles, the floating island's stern guardian.
As Sonic begins to chow chili dogs for a snack, he finds a message in the sack from his mother urging him to head to Speedster Island. When he, his brother and his sister arrive, what they encounter is an ancient sanctuary that is about to be overrun by Robotnik and sold off bit by bit. The Hedgehogs must persuade Bartleby to end his deal to build a resort on the beautiful island and save the people of the village from becoming slaves of Robotnik.
Sonic becomes frustrated that maybe all of their efforts of fighting for freedom seem futile. Sonia suggests that they go to Oracle, the spiritual guide, to put everything into perspective. The Oracle makes a deal with the Hedgehogs, stating that if they can complete this next mission, he will reveal their future. Instead upon arrival in the ancient city, they discover their power medallions are missing and they are powerless.
