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I don't own D Gray Man or any of the information besides the characters Sky and Luna.
Epilogue
There was a being born tainted, taught to be cruel, and there was another, a being born pure, his heart leading him to good. The cruel one was named Sky, she was the daughter of the Devil, she helped her father cause chaos and destroy things on the earth. The pure one was named Allen, he was born a human, but a human with a specialty. He was born with something called Innocence.
Innocence is a substance of unknown composition known by the ancient civilization the first cultivated is as the "Crystal of God". It can bond with certain humans, known as "Accommodators", to form an "Anti-Akuma Weapon", the only kind of weapon on earth that can purify Akuma, saving the souls that are bound to them from being destroyed by the "Dark Matter" that gives them their power.
Innocence, being the polar opposite of Dark Matter, the Earl of Millennium's chosen weapon that gives him, the Noah Family and his Akuma their powers, is also the only substance that can damage the Noah and their Memory. Conversely, this means that the Noah have the power to destroy Innocence.
Innocence is, to a level, sentient, capable of recognizing those who are and who are not Accommodators, and capable of punishing Exorcists who turn their back on God. Innocence can also be rather single-minded when it comes to destroying an Akuma.
It was said that approximately seven thousand years ago, an ancient civilization used the Innocence to defeat the Noah Family battle, with the wielder of the "Heart of the Innocence", killing the Earl of Millennium's first incarnation. The battle, though, was so great, that the earth was destroyed in what the ancient civilization called the "Three Days of Darkness", or the Biblical "Great Flood" from the Old Testament.
The ancient civilization, prophesizing the return of the Earl and the Noah, left behind the Innocence for future generations to find, leaving instructions in one particular piece of Innocence, the Cude wielded by Hevlaska, which began:
"To the future generations...
We are the ones who triumphed over darkness, and the ones who shall soon meet their end. Yet impending doom awaits in the future. Thus, we bring salvation to thee.
Here, we leave a message...
-The Ancient Civilization to the Future Generations"
After the Earl returned, as the prophecy within the Cube said he would, the New World Alliance established the "Black Order", charging it with finding the 109 shards of Innocence, the Accomodators who were to weild it, and to prepare for the battle that would come once again.