One year after the fall of the eggman empire, things have gone back to normal. Sonic and his friends have settled in the Green hills while knuckles and rouge explore the planet searching for treasure.
The chaotix, have relocated to a small suburban neighborhood outside of station square called "metrotown". They were at one time world-renowned detectives known for taking down robots infiltrating the city and investigating special artifacts like the chaos emeralds, from getting into the wrong hands.
But nowadays the only action they get in the small suburban town is finding a missing pet or dealing with a school bully.
Now that the world is no longer in turmoil, G.U.N
has shutdown leaving Shadow the Hedgehog out of the job. In desperate need of hero work, he joins the chaotix as a last resort.
The entire world thinks the new notorious Doctor eggman died in the explosion of the death egg, but he indeed is still alive after escaping in an egg pod shortly before the explosion.
Now isolated for over a year in his secret lab in the sewer system under station square, he plans his revenge on the heroes of the Earth.
Life was seemingly normal yet boring for the shadow at first, but after Maria robotnik's mysterious reappearance, Shadow is yet again haunted by his past, and the chaotix have to investigate one of the deepest mysteries they've ever come across.