This is a Fallout Equestria (primarily) and Terminator crossover.

As the war between Equestria and the zebras pressed on, many members of the Ministries conceived of desperate strategies to end it through magical and technological creations of questionable nature. One of these was Project Infiltrator, a top secret project of the Ministry of Awesome. It's goal: to create a super spy that was the perfect blend of pony and machine. But just as its first subject was ready, the megaspells dropped, destroying Equestria and creating the Wasteland.

190 years later, Crystal Eclair awakens in a world of ruin and violence, completely clueless as to what happened to Equestria and herself. Her confusion grows into horror as she discovers that she is no longer a pony, but now a cybernetic zebra. With no other choice left, she sets out to find answers to her predicament. How will she handle the truth if she finds it? Will she find friends who can help her in a world that trusts no one? And what if those who have done this to her are still out there, eager for her to serve a new sinister purpose?

PS. This is not a Prequel to Broken Steel despite what a couple of websites that link back to this story say.

(Chapters 1 to 12 Edited by Alycorn~(CF), New Editor Double R Forrest. New description credit to Double R Forrest )

This story is a sequel to Change

There are many changeling hives spread throughout a large portion of the world. Wherever love energy is going to be found the changelings will pursue it.

But now, one by one, they are disappearing.

Many hives located at the very outer edges of changeling inhabited lands are vanishing without a trace, Twilight Sparkle's family history has returned to haunt them all as something is hunting the changelings down. But how? And for what purpose? And more importantly, what does this mean for Queen Twilight Sparkle and the rest of the changeling race?

Edited by RC2101_Copey.
Cover Art was designed by Jesuka.
TVtropes Page: http://tvtropes.org/pmwiki/pmwiki.php/Fanfic/ChangeQueenOfTheHive
Physical copy: https://www.fimfiction.net/blog/806366/change-queen-of-the-hive-physical-copy

(Featured on the first day, 6/11/2016. Awesome!)

[Complete! With TVTropes apparently!]
Also, apparently, an animated trailer.

In a world of brass and steam, Twilight Sparkle had thought she had made a life-changing discovery with the invention of the telescope. For better or worse, she was correct.

Now her discovery has not only changed her life, but the lives of those she seeks out in her desperate attempt to contact the only other creature as lonely as Twilight herself.

It all would have been much simpler, but it had to be the one Twilight could only call The Mare on the Moon.

Decidedly not within walking distance, then.

[Featured on EQD before story was meant to be submitted. 4/03/2015]

[Editing team: Southpaw, Wolfvenom, Maskedferret, SwanSong and BluePaladin42, without whom this story would be a fraction of its current state.]
[Special thanks to Novel-Idea for the updated cover]

This story is a sequel to Monsters

You might think that Equestrian nights are but serene exhibitions of Luna's work on the sky. You may believe that you can just lay out on the grass and admire the beautiful stars as a warm evening breeze caresses your mane. And you would be wrong.

Equestria is a magical place, and where there is magic, there is chaos. Dead rising from their graves, inanimate objects coming to life, strange apparitions making your foal cry in her room... sounds familiar? No? Then I'm doing my job right.

I'm Twilight Sparkle, and I work the Night Shift.

This follows canon up to the end of season 2.
Check out the Fanart Repository for lots of awesome Night Shift art!

Featured on Equestria Daily.
Winner of Stories Back from the Read 2013.
One hundred percent approved by Twilight's Library!
Special thanks to Nonagon and Wise Cracker.

In the dark forests of Tramplevania dwells a coven of vampires, led by a deadly draconequus named Discord. For many years, his only interests have been in his own survival, until he stumbles upon a beautiful mare with a heart pure enough to care for a monster like him.

Music to listen to.

Cover Art by IduChan

Alternate Cover Art

More fanart by Whiteheart7
CandySweets90240
autumnruby18

AJ Pony's review

Twilight Sparkle is asked by a child where Cutie Marks come from, and begins investigating. However, what starts out as simple research uncovers shadowy forces at work, and with each new clue, she learns more than she ever wanted to know.

(Special Thanks to Doukzor100 for the awesome cover art! )

(I don't know how, but Marked has been featured! Thank you all so much!)

This story is a sequel to Past Sins

In the wake of the battle with Tirek, Twilight Sparkle becomes fixated on restoring Golden Oaks Library. After all, it was home for her little family of three. But as her attempts to repair the books and tree continuously fail, her friends must take matters into their own hooves. Discord, as the good friend he is, tosses Twilight and her extended family into an unexpected adventure while Twilight's other friends get to work on the new crystal palace.

All together, they'll do everything to ensure Twilight and her family have a place to call home when they reach the end of the road.

This story is a sequel to Past Sins

When pursuing Starlight, Twilight and Spike experienced variances of Equestria, and saw how the river of time could have been different. Now, Starlight has moved in with Twilight, Nyx, and Spike and has begun her studies in friendship. To thank those who have helped her embrace friendship once more, Starlight has created an enchantment that allows the castle’s map table to let anyone glimpse other variances of reality.

The power to ask “what if,” can be a source of great amusement… but for some, the hypotheticals are haunting reminders of what could have been.

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

This story is a sequel to Iron Hearts: Book 4 - Emerald Dawn

An MLP/Warhammer 40K crossover, part 5.

With their plan established and put into motion, the 38th Company begins the long and unwieldy task of planetary defense, fueling the arcane energies that may yet unsteady the Empyrean and spare their fleet from an enemy without number or mercy. The inhabitants of Centaur III and even the abandoned aggressors help where they are able, but as their foes grow in number and destruction spreads across the planet, the war for the Centaur system has become a bloody race against time.
All the while, the grim culture of the Chaos marauders continues to mingle with the enlightened benevolence of their equine allies. Tempers fray and allegiances blur. But the die has been cast: Equestria and the Company will survive together, or be snuffed out together.
And even should they succeed, what future awaits these unlikeliest of friends?
For there is no peace among the stars. Only an eternity of carnage and slaughter, and the laughter of thirsting gods.

ALL THE EXPLOSIONS. JUST, ALL OF THEM.

(Cover art by Ahrimatt)
(This series now has its own TVtropes page!)
(This series is a contestant in the Tournament of Canterlot, a charity event to raise money for Syrian refugees! Go here for details and donations!)