A great evil arrives in Equestria from the stars and a mysterious mare appears, kicking off events that are too big for just one world. A 'round robin' story written by multiple authors.
The four crystals of the world are threatened by a great darkness, and the only ones who can stop it are four unusual mares. Final Fantasy V with ponies and a few twists.
Aradia Megido is a Maid of Time. She is drifting across the cosmos, looking for fascinating and beautiful endings and beginnings. Something calls her across existence to Equestria, into yet another mess of time travel loops and alternate timelines.
A Commissar of the Imperium of Man finds herself working as a diplomat for a rapidly expanding multiversal society headed by ponies. She won't bend the knee just yet, even if peace is on the horizon.