Sleet and Dingo plan to collect the taxes owed to Robotnik from the Duke of Velcronia but keep it for themselves. To avoid the wrath of Robotnik, Sleet and Dingo infiltrate the Underground to corral Manic and friends to the commit the crime and take the blame. The scheme is moving along well for the evil duo until they are caught on tape by Max, Manic's friend, who stops the devious Sleet and Dingo enabling the Duke keep his money.

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.

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.

Sonic, Manic and Sonia find an abandoned baby in an alley and begin a search for the baby's parents. Manic grows particularly fond of the child and decides that instead of taking the baby to a shelter as Sonic and Sonia ordered, the baby would be more comfortable at the Underground sanctuary.

The Oracle advises the Hedgehogs to undertake a mission which could reveal answers about their future. Sonic, Manic and Sonia are thrown into a universe that almost seems to parallel their own, however in this dimension, they are not the in the Underground, the Hedgehogs are the rulers of Mobius. Confused by this world, they begin to explore and suddenly find themselves confronted by a corrupted version of themselves.

The Hedgehogs vacation is interrupted by the news of Robotnik's latest weapon. They are shocked as the submarine melts the icy landscape from under their feet. The Hedgehogs then scurry to locate the lethal submarine before the entire planet is completely submerged underwater.