The history of the Underground is told in detail, from the fall of Mobotropolis to the rise of Robotnik. Included, is a prophecy, as told by the Oracle of Delphius, that caused Queen Aleena to give up her own children so that all people of Mobotropolis could one day be redeemed. As the Queen's children grow and witness tragedy all around them, they soon learn that they are not alone in their urge to fight the evil Robotnik.

Argus, a captain of the Queen's guard, is captured by Sleet and Dingo before he can reach the secret rendezvous where he was to meet Queen Aleena. While listening to a scanned radio message, Sonic, Manic and Sonia overhear that a queen's guard has been captured and robotisized. The Hedgehogs then begin their pursuit to recapture captain Argus from Robotnik and get the information revealing the secret meeting place where they may be reunited with their beloved mother.

Sonic, Sonia and Manic return to their birthplace, Mobodoon, a beautiful, festive town. The homecoming is interrupted when Sleet and Dingo arrive to collect back taxes by order of Dr. Robotnik. Because Mobodoon has no form of currency to pay this bogus debt, Sleet and Dingo decide to raid the village and steal its most precious monuments, including the powerstone, which is the center of Mobodoon's vitality. It is up to the Hedgehogs to get the powerstone back and restore their former home to its previous blissful state.

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 memory. 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, but the two are captured by Sleet and Dingo. Sonic and Manic must then work together to retrieve the power medallion, locate the journals and find the one thing that is most precious to them, Sonia.

Sonic, Manic and Sonia invade Robotnik's lair to retrieve the Hedgehog crest. After the book is reclaimed, they discover that this book contains directions to a scroll that could be an important tool to overthrow Robotnik. The scroll is heavily protected, but Sonic leads the group in the right direction where they eventually encounter the royal Aman-Rapi.

Robotnik announces that he will marry Queen Aleena in a plot to become the king of Mobius. Upon hearing the alarming news and shocked that their enemy will become their stepfather, Sonic, Manic and Sonia become suspicious that this wedding may be a trap and decide to investigate. The Hedgehogs, aided by Bartleby, are hired to play music for the ceremony. Disguised as 18th century musicians, Sonic and his siblings crash the wedding hoping to find the Queen and bring to light this most obvious sham.

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.

Manic, Sonic, 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.

A self proclaimed scientist has come to Robotropolis with a device that will reverse the effects of Robotnik's roboticizer. Sonia, Manic and Sonia attend a demonstration of this new technology where Sonia decides she can use it to help her rescue a friend. Sonic, on the other hand, is skeptical that this machine is the real thing and decides to investigate.

Robotnik has arranged a museum exhibit of the Royal family goblets. Knowing that Sonic, Sonia and Manic will want to reclaim their family's treasures, Robotnik expects the heirlooms will serve as perfect bait to finally capture the Hedgehogs. Sonic and his siblings are aware that this is most likely a trap and devise a counter plan of their own to avoid getting caught.

The newly discovered Emerald Peninsula is a perfect place for Robotnik to add slaves to his empire. Sonic, Sonia and Manic are alerted of Robotnik's plan to transplant the peninsula's inhabitants and turn to a fortune teller for help. The mystic advises Sonia of a pendant that could reveal the answer to stopping Robotnik.

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.