Lightning Dust, after being thrown out of the Academy, comes back home to find she also lost her job, and is offered a chance to redeem herself by catching a vigilante.
When Twilight receives a package detailing the short lives of Celestia's previous students, she finds herself trying to prove that Celestia is not removing her students from history.
Twilight Sparkle has disappeared, leaving Spike alone, and Equestria vulnerable. Spike then sets out for Twilight's Institute for Magical Research to find a new Element of Magic.