One wintry evening, a frozen, half starved and exhausted mare wanders into Ponyville from out of the wilderness. It seems straightforward on how to deal with her, a traveller from a world of humans across the forbidden Void, on an adventure in Equestria. Welcoming her, the Element Bearers try to befriend this mare, aid in her quest, and help her find her way home again.

Things don’t quite work out as planned.

This story is a sequel to Days of Wasp and Spider

Believed dead by their creators, the ponies that will become Celestia and Luna have broken their mental conditioning and escaped into the wilderness. Here they plan the revolution that will free all ponykind, knowing that it is only a matter of time before their ruse is discovered.

Back in their underground arcologies, the ponies' erstwhile masters deal with the consequences of the escape, all the while unaware that something lurking at the bottom of space-time wants them all dead.

A Soot-Covered World, book 2.
Canon species only/no humans.
This story has nothing to do with the Holocaust.
Art by InLucidReverie, used with permission.

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

Anon is happy with Twilight. Really. She loves the ornate castle, the lovely meals she eats, and, most of all, loves Twilight herself. It's so wonderful and beautiful in Equestria that Anon almost forgets she used to be human.

Almost.

My fourth-place entry to the Filly Anon Contest. A different approach to the idea, leaning in a more serious direction than many authors take the concept.

Edited expertly by SirReal.

An homage to stories like The Substitute Demon, ALL GLORY TO THE OVERGOAT!!!, and 1000 Virgin Mares, 1 Frickin' Badass Dark Overdude, Infinite Facehoofing

One thousand years ago, the Princesses Celestia and Luna were blindsided by the return of the Masters of Equus. The cult of power-mad alicorns, thought to have been banished from Equestria forever, appeared in the middle of the Princesses' battle for supremacy, and caged them away. The rest of Equestria quickly fell to their might. Even the fearsome Discord was forced to his knees before them. All of Equestria was enslaved, and an era of misery began.

Now, one thousand years later, a lone unicorn mare has learned of a creature that might be able to overthrow the Masters. A creature immune to magic, overwhelming in size and strength, sealed away for centuries uncounted. A creature of ultimate evil: the Smooze.

Unfortunately for Starlight Glimmer, in trying to ensure the creature's obedience, she modified the summoning ritual a bit too far.

Because of her meddling, the soul of a recently-deceased human is pulled from Limbo, and given life, but not exactly a body. Now he has to help her save the world, or face obliteration.

Not much of a choice, is it?

Inspired by Pen Mightier and Bucking Nonsense, the legends who – to my knowledge – popularized the "human in villain's body becomes Equestria's savior" genre. May your inkwells never run dry.

This story is a sequel to Destinies

Nearly a year has passed since the events that had brought two realms together. Each had kept the other a secret until now, two worlds separated by a certain cartoon. Finally, both are ready to deal with the inevitable complications, to realize the benefits of trade: human technology for Equestria, and magic for humanity.

The Princess of Friendship is convinced she‘s up to the task, while Meg‘s doubts over the true meaning of her cutie mark grow as the two worlds converge.

Read Destinies first. You won‘t have any idea what‘s happening if you don‘t.

Pre-reading and editing by Mitch H, Doggyshakespeare, and darkszero.

Magic is bleeding out of Equestria and into another realm, a realm where magic does not exist. Twilight must stop the flow of magic before disaster strikes. Can the natives of this realm be of help? How do sapient beings function without magic anyway? What's this about a cartoon?

Takes place shortly after season four.

Sunset didn't realize just how different other dimensions could be before going through the portal. Now she finds herself in a world where people never age or grow, they just attend high school forever. Whether she's entered a paradise or a nightmare remains to be seen.

Beyond Earth and beyond the Universe within which Earth exists there is a place full of love; the richest mine of love that can be found, as it is seen by those capable of utilizing it...

Within that place, specifically a part of it called the Everfree Forest, awakes one such creature: a Changeling; specifically, a Changeling who had been a human on Earth the day before. How will he survive in a body that literally needs love for nourishment, while in a world that is now wise to the Changelings' tricks and has branded them evil? Better question: Will he be able to change more than his physical appearance?

These questions are not the only thing that will plague him, for the hows and whys of his arrival and transformation are in a hurry to reveal themselves, and Equestria's heart will stop as it waits for its fate to be decided.

Now with a side story (with more to come) from other characters' POV!
POV: MANE SIX

Blurb

What exactly did Pinkie Pie do during the time she held Discord's power? An Equestrian intelligence officer leaves a message to her successor on what little they know so far. Warning: Superintelligences and existentialism

Author's Note

Inspired by The 21-Second God, though I ended up taking it in a different direction than good ol' Squiddy.

Charlie Stross Was Right.

Vaguely planning more stuff about the Equestrian intelligence services, recontextualizing all the episodes of the series one by one to various degrees. If I end up doing that, this story will end up being one of the capstones. It'll also be a long while before I start it, if I ever do.

Also left two (2) lines from literature in there. It's possible I left even more than that inadvertently, considering I tend to repeat cool things I hear. But if you catch them let me know!