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.

Manic, Sonic and Sonia must end their training early when Robotnik threatens the Oracle and takes a member of the resistance hostage. During the rescue mission, the Hedgehogs fall into trouble and begin to place blame upon each other for everything that has gone awry. Queen Aleena then intervenes with an important message for her children that they must learn to work together and derive strength from their willingness to help others.

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. While Sonia and Sonic are working to uncover another plot of Robotnik they find that the baby is not a baby at all, but an android equipped with cameras to...

On a mission in a distant sector of Robotropolis, the Hedgehogs are informed that freedom fighters have disappeared and are going to be robotisized. Sonic races to save his friends, but he is too late. The group of freedom fighters have been robotisized, including Cyrus' father. Cyrus and the Hedgehogs, now motivated by the injustice of what has happened, attempt to end the construction of the potent sleeper bombs that enabled Robotnik to capture...

Sonic and Manic play a game of virtual reality to enhance their pilot skills. When the two brothers decide to put their practice to use, they fly in a successful mission that intercepts a supply ship from Robotnik. To put the Hedgehogs game to an end, Robotnik decides to invade the simulated world and provoke a less successful outcome for Sonic and Manic. Once the virtual danger of the game becomes a reality, it is up to Sonia to play the game...

The Hedgehogs begin to learn the important lessons of what it takes to be a freedom fighter. The Oracle provides teachers to guide Sonic, Manic and Sonia to develop the necessary skills to recognize the power that comes from within. The Hedgehogs also discover the hidden magical force of the power medallions as they grow to understand that teamwork will serve them best in averting the dangers that await them.

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.

Queen Aleena's royal journals are rumored to be buried under a palace in the city of Tashistan. As Sonic and his siblings scour the city in search of the scrolls, Sonia gets into trouble when she is accidentally knocked in the head during a confrontation, causing her to lose her money. Sonia gets into more trouble when she inadvertently sells her power medallion to a local merchant. A young boy from the village makes an attempt to keep Sonia safe,...

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. The...

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 robotisized, which is a secret that could have the chief banished from the tribe. Manic is then captured and taken from the camp, unbeknownst to Sonic, Sonia and the chief. Sonia and Sonic get to the bottom...