In the midst of her dreams, Celestia receives a message from her long-dead father that a terrible, cosmic power threatens Equestria and the entire world. She fails to fully emerge from her subconscious, however, and only a desperate gambit from within her own mind allows her to warn Twilight Sparkle -- and thereby Luna -- of the impending disaster.
Luna hatches a risky plan to rescue Celestia from the hell of her own subconscious, but in order to do so, she will have to descend into the collective subconscious of Celestia, Twilight Sparkle, the other bearers of the Elements of Harmony, and lastly, that of herself -- a place where the black specter of Nightmare Moon still lurks.
Even if they are successful, a dire threat will still loom in the cosmos. A quest that spans aeons and defies the cruel exigencies of time will be necessary to retrieve the only means by which the horror that still haunts the dark reaches of the aether can be stopped, if indeed it can be stopped, at all. This quest will carry the ponies to an ancient, dead city, long dismissed as myth, locked in a state of eternal revelry, but also of eternal death.
In the end, they will be forced to confront their ageless foe, and they will learn whether the magic of friendship is as mighty as they had believed.

Reader beware: "The Sun Eater" goes into some very dark places. It gets dire, hopeless, and violent, and it touches on themes as far-ranging as the futility of existence, depression, suicide, and addiction. It takes cues from some obvious, and on occasion previously-explored questions of the characters' psychology, but it also delves into some relatively new territory. It keeps a sense of humor about itself, but only as much as is necessary to keep it from becoming so bleak as to be unreadable.