The Cryptids were feared on earth, exterminating the human race. After the Exodus incident, the Medusa Device left a huge dent in their numbers. One Scout however, was not killed, but transported by unknown means, and now must fend for itself in this new land of Equestria.
As a side note, I typically don't plan ahead with my work, I usually just come up with it as I go.
~This story is written post-season four, so I have no idea how Season five will change this.~