This story is a sequel to Left Behind

After defeating the Broken Pony, Nightmare Moon is finally free to begin her plans to retake Equestria and restore it to its former glory. However, she is haunted by the ill portents she had been given and searches for signs of her sisters' fragments or the coming of any new alicorns.

On top of this, the king impedes the alicorn's work at every turn and tries to be rid of her just as frequently. So many things happening all at once and spiraling towards the doom the 'leftover tool' warned her about, but Nightmare Moon is determined. No creature will stop her goal, not even the dregs of Equestria's destroyers from so long ago.

Sequel: Left Behind: Sunny Disposition
Apparently it was scouted and is on EqD too

Nightmare Moon was meant to be released after a thousand years. A momentous occasion for her but terrifying for all the ponies on her day of freedom. She would get revenge on her sister and cover the world in darkness and shape everything to fit it.

That was the plan, at least. Instead, something went awry with the spell and she wasn't released when she was supposed to be. The mare-in-the-moon is brought into a world with stagnated technology, giant cities, and no sign of her sister or any of the other immortals. In fact, ponies don't seem terrified of her at all, and the stay within the core of her powers infused and changed the alicorn's body drastically.

The alicorn had no obstacles left! But...she was also a relic of the past. A past everyone seemed to have forgotten. A past she could no longer look upon.

Artwork by ElkaArt. Link in source.
Big thanks to Kryostase for helping spot errors I've missed.