Title: Through the Shattered Mirror.

Main characters: Twilight Sparkle, Starswirl the Bearded.

Genre: Alternate Universe, Dark, Adventure.

Canonical Placement: Near the middle the chapter a Time of Love a Time of Hate

Premise:
While Twilight and Star Swirl attempt to flee Queen Sparkle's dimension, the Queen instead attacks them just as Star Swirl finishes his spell, resulting in an unexpected result…

Twilight and Star Swirl end up in a universe where Twilight herself was never born. As a result, many things have changed for the worst:

Equestria is in a state of war, Nightmare Moon rules over Ponyville from the Everfree forest with the Canterlot forces just barely holding off her assault's.

Spike was raised by normal dragon' s(think "Secret of My Excess" Spike, but with wing's).

Shining Armor has been corrupted by Nightmare Moon and forced to became one of her "Shadow Guards".
Applejack flead Ponyville with her family after Granny Smith was killed for speaking out against Nightmare Moon. Both she and Big Mac are now conscripted Celestian soldiers.

Rarity left Ponyville with her sister, she currently lives as a Canterlot noble with her sister, her parent’s status are unknown.
Sunset Shimmer is still Celestia's apprentice, while Nightmare Moon has taken Trixie as her apprentice.

Cloudsdale was destroyed during a battle between Nightmare Moon's forces and Celestia's Wonderbolts(only Windigos inhabit the ruin's). Any surviving Pegasi either found refuge in Canterlot or were captured & corrupted by Nightmare Moon and forced to become Shadowblots, Rainbow Dash included(Scootaloo is a trainee).

Due to her way's with animals, Fluttershy was captured and forced to tame and train the creature's of Everfree Forest to obey Nightmare Moon.

Pinkie Pie's whereabouts are a mystery. She disappeared a week after Nightmare Moon took over Ponyville. Strangely enough, Discord’s statue vanished on the exact same day...

Now Twilight and Star Swirl must restore order to this world as well as find a way back to their own timeline...the only problem is: Queen Sparkle is there too, and the time loop's are still happening!