As a serpentine menace marches on Ponyville, an unseen Queen begins to plan her vengeance against the one that had imprisoned her centuries before; for only this accursed pony can stop her from claiming Equestria as her own and enslaving everything she deems to belong under her rule.

As the army continues its invasion and assault on her home and friends, Fluttershy, unable to reason with the slithering creatures known as "basilisks, flies to Canterlot and seeks out the aid of Princess Celestia and Princess Luna. However, she comes to find that they have a more important task for her: one that will push her far beyond her known limits as she learns of her ancestry, and the burden of her forebears.