The story takes place in the not so distant future of Equestria. During the night of the final sign before zap apple season is officially begun the meteors go astray and destroy Canterlot. No one can comprehend what could have happened and many blame Luna as it is revealed that she had a dispute with Celestia prior to Discord's resurfacing and the destruction of Canterlot. After spending months in hiding, Luna is eventually captured in the care of Fluttershy. The two are put on trial for treason and found guilty. The two are sentenced to death but escape leaving the ponies behind to choose their faction. Follow Luna, or stay with Celestia. Meanwhile a dark force is gaining power in the Froggy Bottom Bog. Discord will not be contained.

Twilight has fallen on Equestria, and no one knows what will follow it.