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.

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.

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.

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.

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.

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.

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.

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

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 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.

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.

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.

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.

Robotnik is using the local hairdresser, Doo-bot, to get information on the citizens that are against him. Sonia becomes a victim of the Doo-bots trance during a shampoo and while under the spell, divulges important information that could lead Robotnik to a secret base. The Hedgehogs learn that the Doo-bot is equipped with a recording device and dash to retrieve the tape from the Doo-bot before the secret location is disclosed.

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 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.

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.

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.

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.

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.

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.

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.