Sonic the Hedgehog: Mephiles Strikes Back is the sequel and the story is the final, with a collab game, Me (Benclank) and EdGeorgenCody to finish on months or weeks. With characters are returning: Sonic the Hedgehog, Shadow the Hedgehog, Sliver the Hedgehog, Jet the Hawk and Knuckles the Echidna to against the one and only Mephiles the Dark to return him to the scepter of darkness.
- Sonic the Hedgehog - Sonic is the heroic hedgehog who everyone knows. He is the default story and has the middle diffuculty level.
- Shadow the Hedgehog - The ultimate lifeform with a grumpy attitude, he is unlocked after meeting him in Story Mode and is the easiest story.
- Silver the Hedgehog- A Telekenic Hedgehog who came from the future, he is unlocked after beating him in a boss battle and is the hardest story.
- Jet the Hawk - A hawk who is an expert at extreme gear, he's unlocked after beating him in a race with Shadow, he is the second easiest story.
- Knuckles the Echidna - An echidna who's job is guarding the master emerald, He is unlocked after finding him at the shrine, he is the second hardest story.
- Tails - The two tailed fox who comes in Sonic's story with some helping with Sonic.
- Espio the Chameleon - A chameleon who joins Sonic on his journey.
- Blaze the Cat - The firelish cat who comes in Sliver's story with big helping with Silver.
- Marine the Raccoon - A motormouthing raccoon who helps Silver.
- Rouge the Bat - The master emerald thief bat who comes in Shadow's story with helping with Shadow and E-123 Omega.
- E-123 Omega - The robotic E-123 who comes in Shadow's story with helping with Shadow and Rouge.
- Wave the Swallow - The lady expertiment swallow who comes in Jet's story with helping with the leader Jet and the strongest Storm.
- Storm the Albatross - The strongest albatross who comes in Jet's story with helping with the leader Jet and the experiment Wave.
- Tikal the Echidna - An echidna released from the Master Emerald who helps Knuckles.
- Chaos - A god released from the Master Emerald who also helps Knuckles.
- Dr. Eggman - An evil mad scientist and a villain in Sonic's Story.
- Mephiles the Dark - A result of a failed experiment and the main villain of the game.
- Eggman Nega - Eggman's counterpart from Silver's dimension, He is a villain in Silver's Story.
- Metal Sonic - A robotic version of Sonic, he is a villain in Shadow and Jet's stories.
- Nack the Weasel - Rouge's rival, he is the main villain of Knuckles' Story.
- Amy Rose - The damsel in distress of the game.
- Chaotix - A detective agency who help out the gang in various places.
Dr. Eggman and Metal Sonic are at Eggman's base, with a small blob of goo in a test tube, and a hair resembling that of Shadow's in another one. He presses some buttons and a zap! zaps the tubes. A figure respawns, it is known as...Mephiles the Dark. Eggman tells it to obey him, but Mephiles disagrees and wrecks havoc in the base. He then flees.
Sonic is rushing through Seaside Hill when he sees a blob of goo, out of it came Mephiles, Sonic is filled with surprise, but Amy comes and beats Mephiles with her Piko hammer, causing him to flee. But Eggman sweeps in and kidnaps Amy, as an ever determined Sonic and (secretly) Mephiles chase after him. On the captial city, Sonic meets Tails and sees the Egg Carrier on Wave Ocean, they had gotten on the carrier, but they tried and failed again.