The creation of the Chaos Emeralds began with a single idea: to produce an island for the god Chaos to reside on that was out of the reach of normal creatures. (Angel Island) The Meerah (Master Emerald) was created to keep the island floating in the sky, while the regular emeralds were created to draw and manage the reserve energy created by the effort to keep said island afloat. 

The god Chaos also created three spirits to filter the energy into three different categories: inherently Good, in herently Neutral, and inherently Evil. The Good and Neutral spirits were allowed to roam the world free, only returning to the Meerah to draw reserve energies and filter it. The Evil spirit was drawn into the Meerah in order to not only help control the Meerah's reserve power, but also to keep the Evil spirit under control, so it wouldn't wreak havoc on the world.

These Spirits were also given the task of picking out a being they deemed worthy to inhabit, in order to protect the Chaos Emeralds themselves.

Six of the Chaos Emeralds were kept hidden from the world in the Special Zone, and could only be found by someone who was pure of heart. Or so Chaos believed. But after thousands of years, humans created technology that allowed them to bypass the purity issue and retrieve the emeralds directly.

One human in particular proved to be relentless in his efforts to aquire the Chaos Emeralds to fulfill his goal of world domination. Chaos watched the battles ensue, and eventually a hero emerged that was able to defeat the evil human, as well as retrieve the Chaos Emeralds without the help of technology. (Sonic 1)

Chaos realized that this hero had been infused with the entity that was the inherently Good Chaos Spirit. After the defeat of the evil human (Dr. Robotnik/Eggman), the Good Chaos Spirit, acting under the will of the hero (Sonic), used its power to scatter the Emeralds into the special zone once more.

The god Chaos decided to hide the seventh emerald in the special zone as well. He deemed the hero as worthy of the honor of being susceptible to the will of Chaos.

Up until this point, the only beings in the entire world and history of time that were able to attain a higher, more powerful form, by way of the emeralds, were the chosen Guardians of the Meerah, the Echidnas. But because of the greed of a single Echidna leader, nearly all the Echidnas had been wiped from the face of the planet. Chaos decreed that those susceptible to the will of Chaos (aka, those in whom the spirits of the Meerah resided) would be able to harness the power of the Chaos Emeralds and attain their own higher form.

Then a second time, the evil human sought out the Chaos Emeralds to power a machine that would allow him to dominate the world. The hero arose once more, this time accompanied by somoene of equal purity of heart, but with no Chaos spirit within him. The duo of heroes assaulted the evil human many timies in many battles, and eventually the human met his defeat at the hands of the hero once more. (Sonic 2)

The human wasted no time after his defeat to begin planning once more, and this time invaded the island of Chaos. The human stole the Meerah from its resting place in the Hidden Palace after tricking its Guardian (Knuckles, the sole survivor of the Echidna clan) into thinking the Hero was after the Meerah.

The Guardian attacked the Hero many times, often keeping him from getting to the human long enough for the human to get away. Eventually the human betrayed the Guardian, and the Guardian helped the Hero to defeat the human. (Sonic 3/ Sonic & Knuckles)

During this time, the Guardian was able to harness the power fo the Chaos Emeralds and reverberate this power back into their origin, creating "Super" Emeralds, able to amplify a being's power and give them a higher form whether they were suceptible to the will of Chaos or not, as the power was just that great.

After this event, the Guardian sensed the presence of the Good Chaos Spirit and became the Hero's friend, realizing the purity in his heart. He also agreed to help out the Hero when doing so did not jeapordize the safety of the Meerah.

Years passed, and before long a rip in dimensions was created by the evil human, allowing him to enter and plot to rule an alternate dimensional world. Chaos recognized the alternate dimension as being on the same timeline as his own, as a relative to the evil human had entered his own dimension many years before. Considering it safer for himself and the beings of the world, the god Chaos drew Angel Island into the new dimension, to leave it permanently anchored, and allowing safe transportation between dimensions.

The amount of energy exerted by Chaos to transport his island into this alternate dimension produced unnoticed cracks in the Meerah. When the evil human attempted to steal the Meerah with the purpose of harnessing its energy to power a weapon of mass destruction, Chaos was unable to withold his anger and erupted from the Meerah, causing it to shatter. Chaos was an imperfect being with the Meerah shattered and had no Chaos Emeralds to give him replacement power, but the evil human "collared" him and fed him the emeralds he needed.

Upon obtaining his perfect form, Chaos proceeded to rain chaos upon the alternate dimension, planning to destroy it to thwart the evil human's plans permanently. The Hero arrived in time, and used the excess power that Chaos could not harness into himself to attain his higher form. This higher form was then able to reason with perfect Chaos, and the Good Spirit talked directly to the god. The Good Spirit convinced Chaos to calm his anger and retreat to the Meerah before the Evil Spirit escaped and wreaked havoc. (Sonic Adventure 1)

Unfortunately, during this time, the Evil Spirit HAD escaped from the confines of the Meerah, and had been roaming this new dimension. The evil human had stumbled across some old notes from his grandfather about harnessing spirits for power, and through these notes was able to sense and capture the Evil Chaos Spirit. He held the Sprit captive until he could create a shell.

The evil human uncovered more notes from his grandfather concerning spirit harnessing, leading to a project he had worked on named 'Shadow.' He learned that this project had been created to be the Ultimate lifeform, capable of destroying anything the doctor deemed unworthy. The doctor found Shadow's whereabouts and and released him.

The evil human's grandfather had captured the Neutral Chaos Spirit and imbued the spirit into the body of Shadow. Shadow had lain dormant for fifty years, and in that time had not aged a second. Because of the power of the Chaos Spirit, it was revealed that those imbued by the Spirits were ageless. Shadow began to gather the Chaos Emeralds by his own will rahter than by the will of the Spirit, as the Neutral Spirit HAD no will. Shadow planned on destroying the world to avenge the death of a close friend, but the Hero was able to stop him.

Because the Neutral Spirit had been imbued first, and because the creature that had the power of the first Spirit had so much more practice before and knew of his abilities, AND because he could sense the presence of the Good Spirit, Shadow continually called the hero a 'faker' or an 'imposter.' The paln to destroy the world, however, was abandoned at the last minute as Shadow regained his memory of the final words his friend said to him before she died. The plan was to use the emeralds to power a weapon on a space station to fire upon the world, blowing it apart. When the plan to fire was abandoned, a plan by the evil human's grandfather activated, planning on crashing the space station into the world instead, creating basically the same effect.

It took the combined might of the Guardian and the two beings susceptible to the will of Chaos to stop the space station, and during this time, it was thought that the being called Shadow had lost his life in plummeting to the earth. (Sonic Adventure 2)

However, this was soon revealed to not be the case. The original had been wrapped in a cocoon of Spirit energy and the fall had not killed him, however he had slipped into a coma. The coma caused him to lose his memory when he awoke, but he was able to recover his memory after thwarting an invasion of aliens that looked like him. (Shadow the Hedgehog)

He also found out about the existence of the Chaos Spirits, and that the technology of harnessing and imbuing the Spirits was alien technology.

(WIP)