At the beginning of the story, Sonic is confronting his nemesis, Dr. Eggman, aboard his flagship. Eggman then activated the ships defense systems, activating the cannons and bringing forth a horde of Egg Fighters. After seeing the obstacles, Sonic boosted forward and began dodging the batteries fired from the cannons. Bounding across the flagship, Eggman brought forth his Mech and unleashed a flurry of machine gun fire. After running across the ceiling while dodging missiles, Sonic ran through the Flagship's hallway. Eggman fired his Mech's grappling hook-like arm and grabbed Sonic. After being pulled to Eggman in the Mech's grasp, Sonic summoned the Chaos Emeralds from within himself and became Super Sonic in order to stop him, destroying Eggman's mech, Eggman fled in his Egg Mobile and fled from his Flagship. After chasing Eggman through space and destroying half of his fleet, they finally arrived at Eggman's Research Facility and knocking Eggman himself to the ground. As a trap, Eggman pretends to plead for mercy. When Sonic is close enough, he activates the Chaos Energy Cannon, which traps Sonic in the center and begins drawing the Chaos energy out of Sonic and the Emeralds in a fashion that is clearly extremely painful for him.
