After the chaos of Nightmare Moon's return, Celestia signed Directive 51 in an attempt to maintain order in Equestria. Years later, Manehattan has fallen victim to a mysterious illness, and the city has descended into riots and violence as the abandoned citizens try to survive. A highly trained operative tries to restore peace, but rioters aren't the only enemies out to stop her.

After the events of Fallout: Equestria, the leader of New Pegas receives a letter from an impossible mare, summoning her to the sunken wetlands of the Equestrian Northwest. She embarks on a quest that puts the newly-liberated Equestria at risk while confronting her own troubled past.

Twilight is tired of waiting for love... so she creates a new spell.

After her rainbow mouth prank goes horrifically wrong, Rainbow believes she's the last pony left alive in Equestria; that is, until she gets a knock on her front door.