It had been twelve years since Cole failed to halt the plans of the Army of the Twelve Monkeys. The virus was not designed to kill. It caused random phenotype transformations to occur in those affected. Genetic freaks ran amok on the surface of the earth. Many were torn limb from limb and eaten. Others died within hours, their bodies unable to sustain the changes the virus caued to their systems.
Some with similar mutations banded together, in an effort to survive. They formed loosely-knit tribes, and armed themselves as well as they could. Some of the creatures developed an ability to affect their environment with the power of their minds. Many of the equine phenotype mutants who developed horns shared this ability.
The equine phenotype was broadly shared. Some had wings, some had horns, some appared to be normal ponies. Reptiles were also widespread. However, most of them died early, and with a few exceptions, only those with wings were able to escape the hostilities of this new world.
The ponies eventually established their own borders, defending them with deadly force. Pegasi, with bright blades strapped to their legs, swooped down on intruders. The unicorns could topple entire mountainsides onto invading armies. The earth ponies provided brute force where necessary. They proved themselves a force to be reckoned with.
Outside of their borders, the borders of New Equestria, the populations of the surviving creatures slowly homogenized. A new world thrived on the surface of the planet, even as human colonies remained hidden in vast underground bunkers...
For now, they wait.