In this version of Sonic Unleashed Eggman manages to defeat Sonic, using the tremendous power of the Chaos Emeralds to entrap him. The sheer force of the attack had also broken down the planet into pieces, and released the mysterious dark creature called Dark Gaia from within the depths. Eggman then leaves Sonic trapped along on the broken planet, along with the now-drained Chaos Emeralds. It is now up to Sonic to retrieve and recharge the drained Chaos Emeralds, save the planet, recapture Dark Gaia, and defeat Eggman for good.
The game features both daytime levels, which focuses on Sonic's overdrive speed, and nighttime levels, which are more combat-focused, as Sonic transforms into a fearsome-looking yet powerful Werehog beast, as a side-effect of the Chaos Emerald attack he had suffered from.
The PS2 and Wii versions feature an almost completely new mix of levels as well as a different game engine.