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In Soleanna, the City of Water, lives Princess Elise. Elise is the keeper of a dark secret, the "Flames of Disaster", which involves the Chaos Emeralds. The evil Dr. Eggman learns of the Flames of Disaster and kidnaps the Princess. When the world-renowned hero Sonic the Hedgehog learns of this, he sets off to defeat Dr. Eggman once again, save Elise, and secure the Chaos Emeralds. However, Sonic's quest is soon interrupted by a strange white hedgehog called Silver the Hedgehog, who has traveled from the future to stop Sonic from becoming the "Iblis Trigger"[2] during his journey; the Iblis Trigger causes many deaths in the future from which Silver hails.[1] Sonic must now discover what Silver wants and make sure that he does not interfer in his quest.
Shadow the Hedgehog will also be featured in the game, but his role in the story is currently largely unknown other than that he will be encountering a mysterious fourth hedgehog.[2]