Fluttershy awakens to find herself in a drastically changed Equestria. With powers given to her by the her captors she is rescued by Shooting Star before she can be drawn over to their side. She bears witness to her friends turned to monsters by a highly advanced alien force called "The Cold Ones."

They have overrun Equestrian and the lands beyond subduing all who resist and nullifying magic by mysterious means. Celestia tries to lead the remains of the scattered ponies as they cling to life on the planet below while Luna prepares a weapon on the moon with the few she could bring with her.

Many now rely on Fluttershy to save all of pony kind from slavery or worse, extinction. Now she must balance her sanity, morality, and a growing malice for her enemies, without losing herself in the process.