The wedding of Princess Cadence and Shining Armor was suppose to be perfect, however a certain changeling ruined it all. Upon defeating Celestia and enslaving four of the elements of harmony Queen Chrysalis quickly conquered all of Equestria. With no one to stop his return to the throne King Sombra easily reclaimed his position as King of the Crystal Empire and quickly established an alliance with the Queen of the Changelings. Due to the chaos and the lack of Celestia's magic on his imprisonment Discord was once again released from his stone prison and became an ally to Chrysalis, enabling her to change many things in Equestria to better suit her species.

The ponies of Equestria today suffer from the changelings feeding on them daily while their world is twisted in Chaos from Discord, their only hope being Princess Luna and the 2 elements of Harmony left. But first Princess Luna must find the 2 ponies and then find a way to save Equestria and defeat the 3 most powerful villains in its history.