A Tale of Two Sisters takes place approximately half a century after the natural deaths of the mane six. Once more, Celestia deals with the tower of lies she's trapped herself in, slaving herself to shouldering the government, and the day/night cycle of the world for the lower classes and all beings on the planet, much like Atlas. She also contends with the guilt of her own hunger for power, one that nearly brought an end to Equestria so long ago; guilt for her sister too, who she neglected and mistreated for so long, she who remains estranged to her, shattered in mind and soul.

Omens have begun to creep upon Equestria once more as Celestia begins to see less and less of her poor sister. A ghastly shadow, a whisper in the night, and knife drenched in darkness, ready to strike. A great evil is beginning to advance upon Equestria: and it is not of this world.