The war against Dr. Eggman is underway, but Mephiles plans to make his move, and the greatest battle of time is at hand... Soon, a great darkness shall cover the world, and evils barely imaginable will come into play And Shadow's destiny has only begun.

Shadow and Rouge become married... just in time for all hell to break loose! Mephiles, Shade, and Mauve are back, and from the impregnable Aero Fortress, they cannot be fought, let alone defeated... or will Shadow find a way?

Shadow and Rouge are now well into a romantic relationship. But Shade the Echidna has picked up the pieces of Mephiles' Empire, and seeks revenge. Joining his cause is a deadly bounty hunter: Mauve the Bat!

What starts off as a simple mission goes into a war with a unified empire of enemies... led by one thought to be dead. Shadow, Rouge, Sonic, and everyone else must unite as well to face both old and new menaces.