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.

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 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.