Luna discovers a vast and ancient being approaching Equus. When she and Celestia go to meet it, they see into the early dawn and eternal twilight of their universe.

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Based off of a thought/realization I had in my studies.

_{Illustration "Black Islands" used under creative commons share-alike, which the artist (Equestria-Prevails) put all of his art under.}

Nopony has heard from Fluttershy for three months. Not Rainbow Dash, not Rarity, not even Pinkie Pie. Her friends have been tending to the cottage and her animals, keeping it clean and organized, but even with Twilight's constant magic scans and a semi-constant guard search Equestria-wide, no hint has been found of where she went, how she vanished, or why she didn't tell anyone. Some ponies even think, in their darkest nightmares, that she might be dead.

Then she shows up one day, very definitely not dead, but just as definitely not the same as she was.

And does she have a story to tell. Boy, does she ever...

Coverart by Paladin.

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.

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.

Somepony is sabotaging Moondancer's research project.

Twilight Sparkle suspects Starlight Glimmer may be responsible. She enlists the Canterlot Royal Guard to protect Moondancer, and offers to help with her research.

Soon, however, the two ponies discover an unexpected side effect of Moondancer's research: one with dangerous consequences for all of Equestria—and possibly even their friendship.

Inspired by The Writeoff Association's "Out of Time" contest.

(This story is sci-fi, and somewhat different to regular FIM stories.)
Aneki's world was small. It was spherical, and it only took a day to gallop from one side to the other. She had been taught nothing existed outside the sphere, but she wasn't so sure about that. Perhaps her world was a bottle, a container in which ponies had fled to live. A time would come when she gained the opportunity to investigate these things first hoof, if she lived that long.

==Originally written spring 2011== Equestria Daily Post==
GLaDOS is free of Chell, free to continue testing, when she discovers a portal gun Wheatley tried to repair with duct tape. When the portal gun catastrophically fails, the enrichment center, GLaDOS, and Chell are literally dropped in the middle of Equestria. The mute test subject soon finds the world of ponies far more welcoming than the human world. But GLaDOS sees possibilities. Let the testing begin... for science.

This story is a sequel to Sharing the Night

Twilight Sparkle is the alicorn of the stars, and after a period of self-discovery, ancient-goddess-discovery and a minor case of malmanifestation madness, she has finally come to share the night, a city, her ex-villain status and a bed with Luna, the alicorn of the moon.

Things are looking pretty good for her.

The five demigoddesses she created out of spite? Not so much. Celestia and Celestia are a little lost too, and for some unknown, completely mysterious reason, dragons are flooding into Equestria—and they're not acclimating. Someone probably should do something about that.

It never gets dull in Ponyville, does it?

TV Tropes

Rarity just wanted to curl up with a book with no redeeming values except the prose. But curling up with a friend can be just as much fun.

Man, shipping is very anti-reading right now, isn't it?

Teen because hot mare on mare action isn't for everyone.

Edited by Magicman7997, DictatorDuck, and Evanescyan

Now with a positively fabulous Dramatic Reading, darling!

Do you remember that one time when you and your fashion understudy got drunk and made love? Rarity doesn't.

Cover Art by RuinedOmega