Equestria has faced many threats, ranging from reality-warping draconeqqui to magic-stealing centaurs and the like. But Equestria has never faced the wrath of a god. Celestia, Luna, Discord, they may seem like gods to the populace, but not even the Tree can compare to a millionth of this guy's power.
He looked upon them and deemed them "racist" and "corrupt" nature-abusers before casting his judgement upon all of Equestria, and it is up to none other than Twilight herself to prove pony kind is innocent and convince him to spare them.
Fortunately, she is not alone in this. Both Twilight and Spike will find dark secrets that will change their outlook on how the world works, the history of ponykind way past the events of Hearth's Warming, and even something about Twilight's old mentor and the royal family.
One thing's for certain, things will never be the same after this.