Over 50 years ago, deep in a Military Research Space Station, Prof. Gerald Robotnik forged an experiment known as "Project Shadow" while trying to unlock the secrets of eternal life at the request of the Government. The experiment culminated in "The Ultimate Life-Form"; Shadow the Hedgehog, a creature with the ability to harness the mysterious power of the Chaos Emeralds in ways not thought possible. After being thought dead in Sonic Adventure 2, Shadow returned in Sonic Heroes with amnesia, and still does in this game. In the beginning of the game, Shadow is still without any clue about his past. He does not understand who he is or where he's from, but he's determined to find out, be it from Black Doom, the leader of an alien race who claims he and Shadow made a pact involving the Chaos Emeralds, G.U.N., the militaries that murdered Maria, or Dr. Eggman, the evil scientist.