Fate/Equine Choreia is a combination of ideas presented within the Friendship is Magic universe and the extensive "Nasuverse," or the setting of the works of Japanese game company Type-Moon, known most for their visual novels Tsukihime and Fate/Stay Night. The Holy Grail War, a concept taken from Fate/Stay Night, comes to the Kingdom of Equestria, and phantoms from the past have come to threaten the Kingdom's peace.

Taking place an extended period of time after the events of "A Canterlot Wedding," Twilight Sparkle receives two mysterious packages from an anonymous sender, leaving only the message "FROM ME." The contents of the packages were a bowl and one of Star Swirl the Bearded's many journals, and as evidenced by its contents, it was one of his last. Twilight then learns of the Holy Grail and of Star Swirl's intent to destroy it.

She summons Star Swirl the Bearded after reading an incantation which was found inscribed in the bowl. Insisting on being called Caster, one of seven predesignated roles given to a total of seven Servants to fight for the grail alongside their Masters, Star Swirl explains himself and gives Twilight a brief history lesson of the time before Equestria. He goes on to explain the Holy Grail, the War, and the roles of Servant and Master. In his bid to destroy the Grail, his wish that made him a Servant, Star Swirl implores Twilight to fight with him.