In the 7th millennium of recorded time, the Twelve Colonies of Ponykind are at war with their own creations, the robotic Cyponians. The Ponystar Fleet is on its way to the peace conference when they are caught in a Cyponian ambush. It is a trap, and at the same time the Cyponians launch a nuclear holocaust on the Twelve Colonies. Out of billions of ponies, less than fifty thousand survive. Ponykind is reduced to a wandering rag-tag fugitive fleet led by the last ponystar, Equestria. Hunted by the genocidal Cyponians, with foes within and without, they search for a new home, a shining planet known only from pony legend.

It is all OC ponies - sort of. Several of the characters bear some resemblance to the mane cast, and may be related to them.