Five hundred years after the Discord's first defeat, a lone unicorn scientist makes an interesting discovery. Across Canterlot, over the last few centuries, accident rates have increased in the area around the Royal Palace. His work is ridiculed by his peers, but comes to the attention of the Princesses, who know exactly what is happening: Discord is waking up. With Luna and Celestia, he concocts a plan to stop the Lord of Chaos forever.

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Cover art butchered from UnderwoodART's render of the stained glass in S02E01.
This story is based on S1/S2 (Discord was never released and reformed) and sits within my Soot-Covered World canon, but is stand-alone. No knowledge of the other books is required.

All thanks to ascendant, NoeCarrier, turol, KMCA, Caliaponia and billymorph for their prereading and editing over the life of this story.

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.

Be Awed and Amazed by the tale of Sweetie Belle as she traverses the multiverse in search of her lost mentor and friend, Twilight Sparkle! Will she find her in post-apocalyptic Equestria? Or maybe in a strange world where everypony is the wrong gender? Or even where a Pony claims to be a human? Read as she journeys through very familiar worlds you might have read about... if you dare!

At this point in time all the main worlds to be visited have already been chosen. Thank you all for the suggestions, and I hope you enjoy the surprises!

Here's the official TSC:F Music Intro: The Sweetie Chronicles: Fragments

WDTP: S2/3-CE
You can also visit the TV Tropes Page which has spoilers!

[Third Person]

Commissioned by Canary In The Coal Mine.

After losing his last living relative, Carter Arvil, former CIA Agent turned real estate agent, is approached by a mysterious woman who offers to sell him a magical kingdom. Assuming the woman is simply a little unstable and selling a magical pony styled theme park aimed at little girls, Carter accepts the deal. A deal which immediately takes a turn for the unexpected as the offer was exactly what it said on the tin and comes with several major strings attached.

Like having to be a pretty pink pony princess.

Cover art by https://egophiliac.deviantart.com/

Featured for a frankly astounding amount of time!

After a mirror portal field trip being conducted by Luna goes terribly wrong, Ocellus finds herself trapped in a strange palace far from home. That palace, once abandoned, is now infested with a hive of love-starved changelings intent on using her only way home as a means to invade her world.

Otherwise, Ocellus appears to be alone.

At first.

The story is inspired by, and a homage to, my favorite game of the last decade. However, this story is neither a crossover nor AU. This story is set after "The End of the End" (but before "The Last Problem"), and is purely a My Little Pony story. Warning: rudeness and intolerance are not allowed in the comments, but spoilers are. Exercise discretion. Remain polite and on-topic. And please enjoy the story!

Flitter doesn't like most ponies. There's hardly anything in the world Flitter likes, very few which she can even remotely tolerate, and only a couple which she truly loves. Fluttershy is not in the last two categories. Flitter sees Fluttershy as weak, and weakness disgusts her.

But when you're trying to help someone you love, you'll look for help in a lot of places -- including the cottage of the weakest pony in the world.

And for those willing to listen past their pain, it might be the place where they start to learn what true strength is.

(This story takes place about five moons before Triptych and well after On The Application...)

Part of the Triptych Continuum, which has its own TVTropes page and FIMFiction group. New members and trope edits welcome.

Now with author Patreon and Ko-Fi pages.

Audiobook production by ObabScribbler.

For years, Twilight Sparkle and Queen Chrysalis have been at each other's throats. Both have experienced victory over the other, and both have experienced defeat. Out of all the creatures in Equestria, none despise each other the way the pony Princess and changeling Queen do. They seemed destined to remain locked in battle forever, or at least until one is finally dead at the hooves of the other. The cruel insults, the vicious loathing, and the powerful spells that have passed back and forth between them at each meeting have become the stuff of legend.

Imagine Twilight's surprise when she finds out changelings consider this dating.

And now they're married.

***

Sequel: Pony Courtship Rituals

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Some beautiful fanart of the end of chapter three was done by Dmann892; you can see it here.

More awesome fanart, this time from chapter one.

Now with a TvTropes page (obligatory TvTropes warning goes here).

If you want a Russian translation, you can find it here.

There is now a reading of the story on Youtube, which starts here.

Diamond Tiara becomes an alicorn princess. She gets up to adventures and stuff. Silverspoon is well jel. Also, Celestia has a crush on them. (This story is a parody, obviously. Though I genuinely believe that Diamond Tiara is a character that needs more love. She's adorable.)

Suggest ideas for future chapters here.

Cover picture by Total Krazen.

Over 5 centuries ago, halfway through Celestia's millennium long reign, a rebellious political faction attempts to take over Equestria and start a new pony republic. Celestia is accused of crimes against ponykind and put on trial in an effort to remove her from power. Celestia must defend herself, and her actions, against the conspirators who aim to take over her kingdom. The fate of friendship and the future of Equestria hangs in the balance.

Told through the perspective of Princess Twilight reading the story to Luster Dawn.

Cover art by Decoy the Skeletal Boy:
https://www.deviantart.com/theflamingalberto
https://twitter.com/skeletal_boy