If the player throughout the game gathered all seven Chaos Emeralds, he gets an extra level - Doomsday, which pursues the first ship, and then a giant robot of Eggman. After its destruction along with Sonic Emerald falls into the ocean, but their catches fox Tails in his plane, and together they returned back to the main Emerald Isle Angels Knuckles. Sonic enters the Death Egg and leads to self-destruction of the space station, and then comes into the fight with a huge robot Eggman, uses the power of the Chief of the Emerald. Next Sonic acts alone and on the way to the space has already been raised in the Death Egg, he fought three times with Fur Sonic. Realizing that he was deceived, combined with Sonic Knuckles and help him get to the portal leading to the ancient sanctuary of soaring in the clouds. In a place where kept Emerald - Secret Palace - Sonic again facing Knuckles and join with him in battle. Sonic reaches the caves under the volcano, while 'Death Egg' Robotnik is already starting a new start, and the villain can only capture the main Emerald. On the way Sonic continues to appear Knuckles, Eggman trusts, hedgehog and put all kinds of obstacles. Robotnik, continue to fill their cars all around.
Sonic turns into uncharted part of Angel Island and begins to walk in the footsteps of Dr.