The Hedgehogs receive a message they believe is from their cousin. In the message, a castle is left to Sonia, who revels in the idea of having a castle for the Underground headquarters. Sonic, Manic and Sonia arrive at the castle only to see an old, dark dilapidated structure. Inside the castle, the Hedgehogs all have separate meetings with a mysterious apparition who resembles their mother.

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.

Robotnik organizes a track meet to lure Sonic into a trap. Robotnik is sure that Sonic will not sit out on a challenge of quickness. Sonia and Manic are also aware of Sonic's competitive nature and advise Sonic not to enter the event due to the risk that he may be caught. When Sonia and Manic cannot find Sonic, they head to the race to rescue him. Surprisingly, Sonic does not enter the race, but finds himself involved in a more challenging test of speed - the race to save his brother and sister.

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.

Sleet and Dingo escape the Flying Fortress with the Chaos Emerald. In a fight over who will control the Emerald's power, Sleet and Dingo drop and break the Emerald in two. Instantly, a rash of earthquakes and other natural disasters are sparked by the emerald's energy. Knuckles and the Hedgehogs turn to a relative of Knuckles for answers of how to stop Mobius from being slowly devoured by the emerald's force.

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.

Robotnik's new weapon, Art, is the enforcer of Robotropolis new eradication policy. Art's objective is to destroy everything in sight, including Sonic, Manic and Sonia. The giant mechanical beast is seemingly unstoppable until he overhears the musical melodies of the Underground band.

Sonia is invited to a debutante ball, but before she can be officially announced to society, she and her brothers, Manic and Sonic have an important mission. Robotnik has constructed an evil weapon that will capture and robotisize all members of the resistance all over the world. The Underground must hijack this weapon and insert a deactivating device before the brain of the vehicle is installed. Sonia daydreams about the party, becomes distracted and is caught while executing part of the mission. Sonic aids Sonia to help her focus on their mission and still make an appearance at the ball.

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 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.

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.

Manic, Sonic and Sonia must end their training early when Robotnik threatens the Oracle and takes a member of the resistance hostage.

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.

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.

Queen Aleena advises the Hedgehogs to travel to a valley of Mobius so that they can bring about peace between two contingents of the resistance that have split. In the meantime, Robotnik is able to build a dam that is dangerous to the peoples land because of the lack of a cohesive effort to end the construction.

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.

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.

On a mission in a distant sector of Robotropolis, the Hedgehogs are informed that freedom fighters have disappeared and are going to be roboticized. Sonic races to save his friends, but he is too late. The group of freedom fighters have been robotisized, including Cyrus' father.

On a trip to Port Mobius, Sonic, Manic and Sonia are told that ships are sinking due to the Mobian sea-beast. The legendary story becomes fishy when the Hedgehogs meet Captain Squeegee who informs them of a scam in which townspeople must rely upon Robotnik for protection from the sea monster, when in reality it is Robotnik who is sinking ships, not a monster. Sonic must overcome his fear of water and the monster to find the truth and thereby ending the fears of the sea side town.

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 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.

The Hedgehogs latest quest to find their mother takes them to the prison tower where they encounter a masked stranger who insists he is family. This stranger is actually being used as bait for another attempt by Robotnik to capture them. The stranger creates a rift between the siblings, which leaves the Underground disbanded, vulnerable and ultimately trapped.

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.