Luna's sudden abduction by the ponies of the Apocalypse cause a series of events that eventually make Equestria fall into chaos and under the rule of the New Chaos Republic. The new ruler, Nightmare Chaos, has intentions that are shrouded in mystery.

The Main Six attempt to get Equestria back with the help of survivors. As the events unfold, six new Elements are revealed. Where did they come from? And why did they appear now?

(The events take place after the end of Season 2 and before the beginning of Season 3. )