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.

Robotnik has his sights set upon Queen Aleena's crown jewel, which glows as it is moved closer her. Sonic, Manic and Sonia plan to recover the jewel from the merchant owner before Robotnik, not only to find their mother, but to protect her as well. The Hedgehogs acquire the jewel and begin their search, the glow becomes more radiant the closer they travel to their destination and their hopes of finding the Queen seem to be a tangible reality.

Sonic and his siblings travel to the outskirts of Mobius to recruit a tribe of nomads for the Resistance. The Hedgehogs van breaks down and they are saved by the tribesman. Once they return to the camp, Manic discovers that the chief has been roboticized, which is a secret that could have the chief banished from the tribe.

What is supposed to be a vacation for Sonic, Manic and Sonia turns into a battle to save Mobius when Robotnik attacks with his newest weapon - the Flying Fortress. Sonic investigates the ship thinking the weapon can be destroyed by removing its reactor, however his efforts fail and he goes to Knuckles for help, because he believes the weapon is powered by the Chaos Emerald.

Knuckles reluctantly makes a deal with Robotnik to turn over Sonic and his family in exchange for finding the Chaos Emerald that will save Mobius. Knuckles soon regrets that he ever trusted the evil dictator after Robotnik begins to follow through on his plans to roboticize the Hedgehogs.