When Twilight Sparkle slipped beneath the covers last night, everything had been fine. She had friends whom she loved, a teacher she adored, and a bright future ahead of her. But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.

Everything is wrong and nothing makes sense; even her friends have changed. The doctors keep telling her that she is sick, that none of it was real and that it was all in her head. Yet she remembers a life far beyond the hospital walls. She couldn't have made it all up on her own. They must be lying… right?

Ask Asylum Twilight - Still updating regularly!
Equestria Daily
TVTropes
Asylum Fan Group
The Tartarus Project
Russian Translation
The Asylum 20,000 View Spectacular Stage Show!

Art:
Asylum Cover by conicer
Twilight and Twilight Smiles by dreamingnoctis
Mirror Twilight and Plague Doctor by Jaestring / BloodGoldWings
Twilight Smiles and Doctor AJ by conicer
Nurse Ratchet and Silas and What's in the mirror? by Archonix
Doctor AJ Sketch by Archonix | Colored and vectored version by ReFro82
Twilight's Asylum by Khan the Cake Lover
Smilight by HappySwitch
Twilight Waking Up by Dombrus
Fan Art by toxicdemon10
Asylum Twilight by Madness-With-Reason
Asylum Fluttershy and Asylum Ch 26 by Downburst-Backspace
Twilight and her Twin by v747
Birdgirl by sirValter

Readings and Videos:
Asylum Animated Trailer Video by formuladash
Reading by Gammarobot (SugarCubeRadio): All Chapters Here
Reading by Ender Brony: All Chapters Here
Reading by VisualPony: All Chapters Here
Reading by MelancholyIguana: All Chapters Here
Fan Trailer by Kaidan: Asylum FanFic Trailer Cuckoo's Nest

Sanctuary by Kaidan
Broadhoof Files: Dr. Humors by TypewriterError
Broadhoof Files: Corporal Phalanx Spear (Ret.) by Phalanx Spear
A Hearth's Warming Tragedy by Seven Fates

A special thanks to Breath of Plagues, Rex Ivan,
ChudoJogurt, Cynewulf, Death the Kid, Selbi, PrinceDolph, Blahman2816, Queue, and Gage!

Axan Zenith - Dr. Dreamer
Dratini4 - Way Finder
psychicscubadiver - Bright Mind
Velkaden - Dream Chaser
Reese - Silver Glow
Viola Heartstrings - Clover
Archonix - Spinney Whiteacre

Years after the Stable Dweller's journey to restore Equestria the world is still slowly recovering. Many parts of the world remain radioactive Wasteland despite the efforts of the NCR. In the far flung northeast region around the former city of Detrot the land remains a harsh, violent place. Living in a secluded mountain valley at the edge of this region, Longwalk is a colt ignorant of the larger Wasteland. His tribe has lived in isolation for generations, and he knows nothing of the world beyond the ten miles surrounding his remote mountain village.

All of that is about to change. Dragging a friend along to explore beyond the boundaries his tribe's laws allow, Longwalk makes a startling discovery; one that prompts a journey of his own out into the Wasteland with a mysterious unicorn filly at his side. Before he knows it Longwalk is caught in a dangerous web of Wasteland politics, powerful pre-war organizations, ancient death-filled ruins, and a growing cadre of unusual companions... each with secrets of their own.

Based on the wonderful Fallout Equestria by Kkat, and the Wild Arms video game series by Media Vision.

Pre-read by Doomande, an all around awesome dude.
Cover art by SpyroConspirator, a very talented artist.

Completed side-story featuring Crossfire found here.

After a mysterious and widespread spell causes ponykind to vanish, Fluttershy is left behind to cope with what the future has in store for her and the remains of Equestria.

In a matter of days, the once-prosperous nation begins to descend into a harsh and unforgiving place. While cities crumble around her, Fluttershy finds herself living in a land rife with dangers and heartbreaking reminders. With nopony to turn to, Fluttershy is forced to learn to fend for herself, discover what happened, and, if possible, find a way to reverse it.

Survivor Shy is an illustrated story following Fluttershy in the weeks after a magical cataclysm. While the last pony relives her past, readers are offered a vivid glimpse into Fluttershy's mind and are led on a harrowing journey through the ruins of Equestria and beyond.

Story branches out before Season 3 Finale.

In-progress Reading by Finish Line available
In-progress Russian translation by Papilion_star available.

The following transcripts are of a journal found in Ponyville on April 16th of this year. The last recorded contact with the town had been 3 days prior, on the 13th, when a team under orders from Princess Celestia was sent to look into several missing pony reports in the area. When another group of investigators were sent on the 16th, the town was found deserted. The journal’s owner is believed to be the princess’s personal student, Twilight Sparkle. None of the town’s inhabitants have been located in the weeks since.

Readings:
Nimbus Productions
Scribbler Productions

I highly recommend both of them.

A print version of all the stories in this series can be found here.

The world's going to end in one week. It's been doing that for a while now.

Someone in Equestria's broken the world. They've taken time along with it, trapping everything into a single, indefinitely repeating week. Only the elements' bearers move forwards in time, but they've got problems of their own. For each cycle drains their talents from them, each conversation twists old friends into enemies, and not a single one of them knows how to save the world. Some of them have even stopped trying.

And then Twilight finds a way. All that's left to do is gather everyone back together.

Story arcs written about an apocalypse cycling in perpetuity and the effect it has on Equestria. Not as dark as it tries to be.

Additional: Story formatted to look its best in Font Serif, Size Normal, Colour Medium-Dark, Paragraph Spacings 1.2; this as the banner image; no interactive pony, Snow Default, css color #8c8691, Background Pattern Stars and Background Image Night Town . Reading otherwise will expose you towards rogue spacings, silly typography and a severe lack of Luna.

Featured on EQD for crimes against humanity.

Have you ever had a dream that just seemed so real, that it was impossible to say for certain that it was even a dream at all? A dream that, despite all of its impossibilities, seemed to re-write your entire perception of reality, re-writing your sense of what—and indeed, who—you are? Accepting change is hard enough as it is. But when you're a somebody who wakes up as a somepony, how do you cope with the impact such a drastic change has on your mind and body? With changes like these, it must surely just be a lucid dream—albeit a suspiciously accurate one—just brimming with potential and ripe for exploration. So you might as well suck it up and make the most of these distressingly…unusual circumstances, and seize this psychological adventure before you wake up and the dream ends.
After all, this couldn't possibly be real, so the dream must come to an end eventually…right?

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

Scootaloo has always looked up to Rainbow Dash as her friend, her inspiration; Even her big sister.
But as tragedy comes to prove, everyone must eventually say goodbye to their idols at one time or another... sometimes unexpectedly... and carry on their loved one's legacy.

In this tragic tale, Scootaloo will realize that life is a precious gift that can be taken away in the blink of an eye... or in the flap of a wing.

(Credit to http://knifeh.deviantart.com/ for picture and idea)

Reader, in ancient days, the old lords of the world numbered in thousands. Then hundreds. Then even less.
Now, they are found only in tapestries and fanciful ballads.
The creatures are all vanished. All but one.

Rumors say there are more of him, somewhere far away. A young and supposedly gifted mage called Star Swirl, and Heartstrings, a gentle spinster, have joined him on a journey to find the rest.

Featured in The Royal Guard's Fic Spotlight #5
TV Tropes page (that could use more love)

Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.