Some years after Twilight has taken her position as Princess of Equestria, but before Luster Dawn becomes her student, Equestria is at peace.
All is not to remain that way; the return of the Windigoes ancient magic cracked the boundaries of reality, allowing an ancient force to return, one that challenges the very foundations of the world of Equus and all it is built upon.

Faced with a new foe unlike any they have faced, and one able to absorb even the greatest of magic turned against them, Twilight and her friends embark on a desperate quest to a land that was myth even in Star Swirl's time, in the hope of finding a way to save their nation, and their world. At the same time, their friends, allies, and relatives work at home to try and survive, and hope that Twilight and her friends have something to return to.
The journey will take them further than any of them believe, and at the end, more will have changed than any of them could imagine.

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Slight AU set after the end of Season 9; AU aspects only relate to some minor backstories for a villain, and my own interpretations and ideas on how magic works in Equestria, and that Equestria is one nation on a world of many, as well as Equestria having armed forces - of a sort.
The story is an adventure piece, with sci-fi elements, bloody and grim warfare, and - eventually - tech in Equestria, including mecha. Caution for occasional bad language and acknowledgement of adult themes.
While it isn't set after The Last Problem it does hint towards that being an outcome in numerous places.