Before his defeat Discord sealed much of his power away in a book. This book was so saturated with chaos magic that it could alter the very fabric of reality. So the princesses sealed it away in the bowels of the earth hoping it would never be discovered again. So the book lay there in wait to one day spread it's chaos over Equestria.

For the case of the story, assume that Princess Platinum, Commander Hurricane and the founding of Equestria the way Hasbro portrayed it never happened. Same with Celestia banishing Nightmare Moon, as well as Discord being turned to stone by the Elements of Harmony. If you have questions about what will be going on in this story, feel free to send me a PM.