A body has been found in Ponyville. Nopony knows who she is, or who murdered her.

Mint Blossom has always had a difficult life, but when she discovers she possesses a strange power, her life is changed for the worse.

The Mane 6 are ponynapped and taken to a secret base somewhere far from Ponyville. A secret organization, know as the EAAE force them into training for an epic pony war expected in the near future.