The fate of Equestria hangs in the balance as, one night, Canterlot Castle is assaulted, and conquered, by the combined powers of Chrysalis and Discord. Using dark and twisted sorcery, they take control of Celestia's mind, and use her to frame Luna and the Elements of Harmony for the attack. The fate of Equestria seems bleak. It's fate rests in the Hooves of the Lunar Princess, who must travel throughout Equestria to find the new weilders of the Elements of Harmony, and unite them to save their home.

Inspired by the video, "Friendship Was Magic," Discord and Chrysalis return, and take down Canterlot Castle. Luna, who saves Twilight from the Castle, flees to the Ancient Ruins in the Everfree Forest. From there, she must save her empire.