Celestia wants Twilight and her friends to loosen up a little bit around her. Luna just wants to try the hard cider. During a surprise visit to Sweet Apple Acres at the tail end of cider season, Princess Luna has just a bit too much to drink, and when she makes a rather inappropriate joke, Twilight comes to the very uncomfortable realization that she has never seen Celestia excuse herself to use the restroom.

An ordinary afternoon at Canterlot's Summer Sun Faire becomes extraordinary when a young filly gets too curious and Princess Cadence experiences every foalsitter's worst nightmare. This is how one Princess discovered there is more to Twilight Sparkle than she ever imagined, and realized she is truly anything but "a regular old unicorn."

EDIT: Featured on Equestria Daily on 12/31/12. It's a New Year's miracle!

Centuries ago, Clover the Clever recorded in her personal diary the events surrounding the origins and early lives of Celestia and Luna. Now, thanks to the princesses' gracious consent and the scholarship of Twilight Sparkle, this account may now be read by modern Equestrians.

It had been one year since Twilight Sparkle vanished in the battle against the evil unicorn Xander, and her friends were still trying to overcome the grief of losing her. On the anniversary of her presumed death, her friends gather at her memorial. What was suppose to be a day of remembrance was shattered by a strange metal object that landed right beside them. Their anger quickly turns to shock as a familiar unicorn emerges... and boy does she have a story to tell.

Rated Teen for violence, language, and sexual content. Rating and tags may change in future chapters.

This is not a Halo fic. It IS however loosely inspired by Halo as well as Star Wars, Mass Effect and several other sci-fi movies, books, and games.

Edited by Jack-Pony, HuskSummers, Coldwall, and sadron

Cover art by Sonic Rain

No knowledge of TRON is necessary to enjoy the story.

Ten years after Celestia disappeared with no warning nor trace, Twilight Sparkle receives a message from the lost princess calling for help. When Twilight and Rainbow speed to Canterlot, Dash is accidentally transported to a strange world – but in her race to escape the System, she faces an enemy she never expected.

Cover art by Maxiima and RBDash47

Spanish translation by Spaniard Kiwi

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.

For almost a year now, Trixie has been sending letters to Twilight. The only problem is, Twilight hasn't gotten a single one... until today. But now that she has, Twilight is left with more questions than she knows how to answer. Fortunately, she has a plan. Unfortunately, she doesn't know if that plan will work.

Featured on Equestria Daily
Reading by: WhoLandon
Reading by: PonyFicsOutLoud

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

When she catches a bad case of pegapox, Rainbow Dash cannot fly up to her cloud home. Grounded and quarantined in Ponyville, she is taken in by Rarity and Sweetie Belle, who vow to nurse her back to health. Can the pegasus survive her well-meaning caregivers long enough for Twilight to find a cure--and why is the weather turning so weird?

This story is a sequel to Past Sins

Hearth's Warming is a time for friends and family to come together, celebrate harmony, and welcome the new year. Nyx is looking forward to just this as she rides the train to Canterlot with Spike and Twilight. She's going to meet her extended family for the first time and wants nothing more than to make a good impression. Yet, the sheen of the holidays can't hide the trouble caused by meddling grandparents, relentless reporters, and a paranoid uncle.