The three-creature crew of the Peony, a mining and haulage ship running routes in the distant Reaches, finds a distress beacon emanating from a derelict ship. But what they find, thousands of light-years into deep space, might have been better left adrift.

Mayor Mare has a bathroom on the other side of Town hall she likes to visit for the privacy. However, one day she finds a door that previously didn't exist in the hall leading to. It is locked, and so she makes efforts to find out where it leads and how to open it.
Unfortunately for her, it goes places that aren't anywhere near Ponyville, and are dangerous to her home. As mayor, she has a duty to make sure that it remains closed, and the visitors from the other side can't get through.

Scootaloo gets her chance to pilot the experimental Absolution into deep space for its maiden voyage, but not all is well. Halfway through the one year mission in isolation, her ship is beset by Ghosts who hound her every step. The shipboard AI, Star Mother, is struggling with some outside invasion Scootaloo does not understand, and in the midst of it all... something is wrong at the heart of her ship. Something sinister is hiding in the circuits and mental pathways of Princess Luna's greatest and most secretive project: AfterPony. As the Absolution descends into darkness, Scootaloo must come to grips with the nature of a Ghost and the AI who she calls friend.