Ever since she performed at the Helping Hooves Music Festival in Ponyville, Coloratura has begun to modify her music and shows to reflect her true self. As she makes preparations for her new tour, ponies in Canterlot are found turned to stone.

A Haunting in Canterlot is told through a series of vignettes, each focusing on different groups as they try to solve the mystery of the petrified ponies and who, or what, is behind it all.