When Orbot and Cubot discover a group of rejected Cubot prototypes hiding in the jungle, they seek the help of Sonic and Tails to protect them from Eggman.

Knuckles tries to make amends for a past misdeed, but he only succeeds at making things worse.

Sonic and Tails are working on an invention to make Sonic even faster. Unfortunately, Sonic goes so fast that he eventually disappears. Tails is nervous. Did he disintegrate Sonic? Meanwhile, Sonic is alone in another plane of existence where he can only see ghostly images of his friends but can't communicate with them. When Eggman decides to attack, the gang battles him while protecting Tails so he can work on a solution.

The good people of the Unnamed Village feel that things have gotten pretty lawless. They figure there's not a lot they can do to stop evil, so they license, regulate, and tax it. Eggman fails the evil test and must wait 90 days to do evil, so Eggman decides to use Orbot as his front. Orbot will get an evil license and Eggman will be the puppet master. But Orbot's ego gets out of control and Eggman must get Sonic's help to defeat The Evil Dr. Orbot.

Knuckles is upset when he wins a lamp in a raffle and it dawns on him that he doesn't have a home in which to keep it. He sets out to rectify the problem by getting a job.

When the people of the Unnamed Village find out that their village used to be called "Badgerville" after Sticks' evil ancestor, anti-badger sentiment runs rampant. They decide to rename the town to something more agreeable, and an election is held. Eggman buys votes and is able to rename the village Eggman City, then uses a hidden clause to seize power and become a worse tyrant than Sticks' ancestor. In the end, Sticks saves the day, takes back the village, and renames it Hedgehog Village, after Amy, the friend who stuck by her.

While Tails tests his teleporter on himself, he finds himself in the body of a Bee Bot. Sonic must figure out how to reverse the process.

After a failed experiment, Eggman transforms himself into an adorable creature every time he gets angry.