

The Green, Blue and Yellow Chaos Emeralds are found in Westopolis. Shadow retrieves the Chaos Emeralds, hoping he can regain his past with them. The Chaos Emeralds are revealed to be the reason why Black Doom took part in Project: Shadow, to gain them for a plan of his own, warp the Black Comet to the surface and use the humans as a fuel source for the Black Arms. All of them are given to Team Sonic and then used to become Team Super Sonic and defeat Metal Overlord. The Chaos Emeralds are recovered one by one by each of the teams, the Blue Chaos Emerald was recovered by Team Sonic, the Green and White Chaos Emeralds were recovered by Team Dark, the Yellow and Purple Chaos Emeralds were recovered by Team Rose and the Red and Cyan Chaos Emeralds were recovered by Team Chaotix.

Knuckles uses the Master Emerald to shut them off and they are lastly used by Sonic and Shadow to become Super Sonic and Super Shadow and defeat the FinalHazard. Eventually, it is taken by Eggman and all of them cause the ARK to fall toward the Earth. The last remaining Yellow Chaos Emerald was given to Tails after he saved Station Square from Eggman's missile attack and used to power his Tornado 3 and Cyclone machines. They are then used to fuel the Eclipse Cannon and blow up half of the moon. The three remaining are taken by Rouge on Prison Island, and are used by Shadow to teleport them to Space Colony ARK. gets ahold of the other four and the Blue one is given to Rouge the Bat, who later gives it to Eggman. Eggman, who uses it to resurrect Shadow, and the Green Chaos Emerald was put in a bank, but it was stolen by Shadow soon after his release. The White Chaos Emerald is somehow obtained by Dr. However, they are always thwarted by Sonic the Hedgehog. Eggman for years, hoping he can use them to power his doomsday weapons. The Chaos Emeralds have been the target of Dr. 1.8 Sonic Chronicles: The Dark Brotherhood.
