Sneaky Dr. Eggman managed to steal the final Chaos Emerald after his battle with Tails, and now has full power to the Eclipse Cannon not knowing that the weapon was disabled by Sonic. Once the final Emerald is installed in the control console, the Ark sets off on a collision course with Earth. Realizing this, Eggman and Rouge join forces with Sonic to stop the Chaos Energy powering the reactor core.
Upon arrival in the chamber, Sonic and Knuckles encounter the Biolizard, the original ultimate lifeform prototype. Shadow arrives to take on the monster while Sonic and Knuckles head to the shrine to deactivate the Chaos Emeralds. Not willing to give up, the Biolizard uses it's own version of Chaos Control to merge with the Ark and continue the plan to destroy Earth. With no other options, Sonic and Shadow use the Chaos Emeralds to transform into their super forms and battle the Final Hazard head-on...