Chaos Emeralds are magical gemstones containing unlimited power. They previously existed all over the universe, until the Great Harmony, caused by the Chosen One, sent all of them into the Zone of Silence. The thousands of existing Chaos Emeralds were then merged by Feist to form seven different coloured emeralds: green, cyan, blue, red, purple, yellow and grey. Chaos Emeralds have been the centre of conflict on Mobius for thousands of years, from Forgotten War during the reign of Mammoth Mogul and his Order of Ixis ten thousand years ago, to the recent battles against Dr. Ivo Robotnik's ten year domination of the planet.
The green Chaos Emeralds on Mobius were a by product of the Xorda's attack on Earth, when their Gene Bombs' massive energies were release into underground beryl deposits. The attack resulted in billions of tons of ash being hurled into the air. Nearly 2,000 years later, the sun finally broke through the dirt and ash. Around this time, the beryl deposits had formed into Chaos Emeralds. The green Chaos Emeralds emerged and rained down on the planet, wiping out the Mobosaurs with the exception of the Ancient Walkers who managed to control the Chaos powers, eventually becoming one with the Chaos Force. One of the Chaos Emeralds had also embedded itself into the chest of Mammoth Mogul, granting him immortality.
Over 400 years ago, the great-grandparents of the Echidna scientists Kayla-La and Jordann discovered a White comet on a collision course with their city Echidnaopolis. The society decided to use the power of twelve Chaos Emeralds to lift their city off the surface of Mobius into the sky. The comet struck the city's former site on the continent of Downunda, after the city had safely ascended into the sky. Some time later, the two scientists' great-great grandchildren, Edmund and Dimitri decided on a plan to slowly drain the power of the emeralds to lower Echidnaopolis back into its former site on the planet. Unfortunately, the Chaos Syphon created by the scientist brothers ended up sending the power into Dimitri, when he attempted to proceed with the plan despite the High Council's vote against it. All but one of the twelve emeralds were destroyed as a result, though this one emerald managed to keep the island afloat.
When A.D.A.M. enacted his plan to draw all of the Chaos Emeralds from around the universe to Mobius, his plans ultimately allowed Tails, the "Chosen One", to fulfil the prophecy of producing the Great Harmony. While A.D.A.M. was distracted, Shadow assisted Tails and opening a portal to the Zone of Silence. There, Tails sent all of the Chaos Emeralds where they would be safe and out of reach from villains, thus fulfilling the prophecy set out by the Ancient Walkers.