Sonic and Dr. Eggman are good friends. However, when Dr. Eggman realizes that his new creation, the Gizoid, could be turned into a world-conquering robot, he goes insane and forces Sonic and some of his friends to flee to a distant part of their world. Eggman and his Gizoids take over their old home and enslave anyone who didn't manage to escape. Sonic and his friends form a rebellion to stop Eggman and save their home!
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- Sonic the Hedgehog - Sonic is a 16 year-old hedgehog who used to be friends with Dr. Eggman, until the doctor went insane. He is extremely fast.
- Miles "Tails" Prower - Tails is Sonic's 8 year-old friend. He is a fox with two tails, and, using his two tails, has the ability to fly. He is also very skilled in mechanics.
- Knuckles the Echidna - Knuckles is Sonic's 17 year-old frenemy. He comes from a long line of Echidnas whose jobs are to protect the Master Emerald.
- Amy Rose - Amy is a 12 year-old hedgehog with a huge and almost obsessive crush on Sonic. She has a large Piko Piko Hammer which she uses when Sonic refuses to go on a date with her. Her angry is the one thing Sonic fears.
- Mel the Mouse - Mel is a 12 year-old mouse and a good friend of Sonic's. He usually works with his friends Lucy, Arthur, and Jake, but also works with Sonic and his other friends.
- Lucy the Mouse - Lucy is Mel's 12 year-old friend. She is also very close to Amy. She has shown romantic interest in both Mel and his other friend Arthur.
- Arthur the Hedgehog - Arthur is Mel's 11 year-old friend. Unlike Mel and Lucy, he's not very close to Sonic and his friends, and prefers hanging out with Mel, Lucy, and Jake.
- Jake the Chameleon - Jake is Mel's 12 year-old best friend. Like Arthur, he's not very close to Sonic and his friends, and prefers hanging out with Mel, Lucy, and Arthur.
- Cream the Rabbit - Cream is Amy's 6 year-old best friend. Despite her young age, she is quite clever and adventurous, however she usually stays in hiding while the crew go into battle with Eggman. She is followed around by a Chao wearing a bowtie known as Cheese.
- Flicky - Flicky is a skilled bluebird and a friend of Sonic and Amy. She is the leader of the Exemption Crew, a small team that is part of the Freedom Fighters.
- Johnny Lightfoot - Johnny is a swift rabbit and a close friend of Sonic. He is the fastest member of the Exemption Crew, but is quite hotheaded.
- Tux - Tux is a penguin and a close friend of Sonic. He is young and naive, but his small size helps in spying missions.
- Chirps - Chirps is a chicken and a close friend of Sonic. He is very skilled with machinery and usually designs devices for the Exemption Crew to use.
- Sally Acorn - Sally is a squirrel and a (very) close friend of Sonic. She and Sonic have had an on-off romantic relationship. She is very good with weapons and usually helps in battles. Despite both having a romantic interest in Sonic, she and Amy are good friends. She has also shown interest in Johnny Lightfoot.
- Porker Lewis - Porker Lewis is a pig and a close friend of Sonic. He, like Tux, is very young and naive, and the two usually work together.
- Joe Sushi - Joe Sushi is a walrus and a close friend of Sonic. He is very smart, and is never part of a battle, instead staying behind and helping Chirps or making plans.
- Dr. Eggman - Dr. Eggman is an insane scientist who was previously good friends with Sonic. However, after he went insane, he took over the area where they used to live and forced Sonic and his friends to flee.
- Mighty the Armadillo - Mighty is the 16 year-old leader of Team Chaotix. He, alongside the rest of his team, was unable to escape before Dr. Eggman took over, but, with help from Emerl, the entire team is able to be spies for Sonic's crew.
- Emerl the Gizoid - Emerl is a Gizoid created by Dr. Eggman. Unlike the rest of the Gizoids, he managed to escape being reprogrammed, and works with Team Chaotix as a spy.
- Vector the Crocodile - Vector is a 20 year-old member of Team Chaotix. He's the strongest of the group, but is somewhat slow (in speed and brains).
- Espio the Chameleon - Espio is a 16 year-old member of Team Chaotix. He's the smartest of the group, and is usually the voice of reason between him, Vector, and Charmy.
- Charmy Bee - Charmy is the 10 year-old youngest member of Team Chaotix. He is extremely small and fast, meaning he is usually used to relay messages from Mighty and Emerl to Sonic, but is quite dimwitted.
- Gemerl the Gizoid - Gemerl is the leader of the Gizoids. He suspects that Emerl is a traitor but is unable to prove that this is true.
- Vanilla the Rabbit - Vanilla is Cream's mom. She was unable to escape from Dr. Eggman, choosing to save her daughter instead, much to Cream's dismay, however Sonic, Tails, Knuckles, and Amy quickly made it a priority to save her.