When Rainbow Dash stumbled upon the hidden desert estate of Star Swirl the Bearded and his family while scouting for a new Wonderbolts training course, she thought it would just be a quick stop. Instead ,she found herself being recruited to fix a blackout and keep an eye on Star Swirl's precocious daughter, Nyx, while Star Swirl goes to some other world to fetch parts for a broken machine.

One mysterious earthquake later, Nyx has disappeared and what few clues can be found point to her being kidnapped and taken into one of the book worlds where Star Swirl's former apprentices, Cirrus and Archeon, had been sent to atone for the crime of destroying most of Star Swirl's research into alternate realities. With Spike at her side, Rainbow Dash must enter the prison worlds of Monolith and Ka'utani to search for Nyx, the apprentices, and the solutions to a whole new gauntlet of puzzles.