Sequel to The Republic.

After peace negotiations fail, the Lunar Republic falls back from Ponyville and into Appleoosa. Of the Mane Six, Luna's supporters decide to stay in Ponyville while Celestia unleashes the Royal Guard on the small town. The ensuing massacre leads to civil war, where Premier Luna uses her powers of state to build up an army to face Celestia's growing regime, the Solar Empire.

Through it all, Discord tries to protect Fluttershy from the brutality of the war by hiding the truth from her, and Twilight Sparkle begins a new religion recognizing Celestia as a divine being.

Sorry for the poor description.