MLP meets Rozen Maiden meets Highlander. Naturally, that’s me never having seen Rozen Maiden or Highlander. But I do know about them! :D
One day, while Twilight is visiting Canterlot, she is attacked by the female unicorns there. She discovers that only one female unicorn in all of Equestria can survive, according to the whim of "Alice," a mysterious mare speaking directly to their minds. When she returns to Ponyville, she discovers that it is practically a smoking ruins, with only a handful of female unicorns alive. One of them being Rarity. There can be only one.
(This is never going to get "dark" dark. However, it is about a war between every female unicorn in existence, and that was the best tag I could pick.) :P
(And with 13 characters, I can't tag them all. ;_; I've tagged key characters so far. Perhaps the tags will change as the story goes on...)