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.

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.

The Hedgehogs begin to learn the important lessons of what it takes to be a freedom fighter.

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

Sonia travels to east Mobius to visit her friend Mindy at the LaTour Estate. After being given a watch by her friend Mindy, Sonia discovers that these popular timepieces are really monitoring devices for the Robotnik Intelligence Agency and are mass produced by Mindy's father Mr. LaTour. Sonia, Sonic and Manic confront Mindy and LaTour with this discovery. Realizing the error of his ways, Mr. LaTour ends production and decides to flee with his daughter. The hedgehogs skillfully put the spy devices to their own use to help the LaTour's escape.

The sinister Robotnik blackmails Cyrus, an old friend of Sonic's, by holding his father hostage. Robotnik makes Cyrus gain the Hedgehogs trust and then has Cyrus convince them to save his father. Cyrus reluctantly informs Robotnik of the rescue plan so Robotnik can devise a trap for the Hedgehogs. However, once Cyrus sees the Hedgehogs helping the kids of Mobius, he realizes assisting in the capture of the Hedgehogs is a bad idea. Instead, Cyrus helps the Hedgehogs and in the process they destroy another of Robotnik's swat-bot factories.

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.

While lost in the wastelands of Mobius, Sonic, Manic and Sonia stumble upon an oasis called Lake Valley Resort. Although Sonic is impressed with the beauty of this safe haven, he has a sinking feeling that this village may be under the scope of Robotnik's radar. Sonic's doubts are confirmed when he overhears Stripes, the leader of the village, informing Robotnik that the Resistance is in town.

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 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.

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.

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.

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.

The Hedgehogs converge on the Floating Island, in their latest attempt to find their Mother. Sleet and Dingo also have an interest in this island that involves the Chaos Emerald, which is the island's life-force. But, before either party can achieve their goals, they have to get through Knuckles, the floating island's stern guardian.

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.

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.

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, 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.

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.

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.

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.

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.

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.