The story takes place a some number of years after the events of S4.

Twilight's studies of harmony detect a magical disturbance in Zebrica. She decides to investigate, and meets up with Zecora in her homeland. There is evil afoot here, one that goes back to the dawn of time, one that neither Celestia nor Luna could erase.

Zecora isn't sure that Twilight is ready to see true evil, in all its unholy glory. Can someone raised in harmony truly comprehend the horrors of the world outside?