Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

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 But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.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

(The Redone Version) (EFH has it's own TV Tropes page! Thanks to redandready45! )

A human has been teleported to Equestria after a lightning bolt struck him. The ponies of Ponyville had never seen anything like him before. Full of fear and uncertainty, all of Ponyville, except for the Mane 6 and Spike, avoided him. The human, with the help of the Mane 6, must earn Ponyville's friendship before a way back home is found.

Rated Teen for some language and mild peril.

Twilight never cared much for romance, but after falling for Rainbow Dash, she's ready to make her move. But what happens if those feelings are unrequited? Should she hold onto hope? Is it even possible to let go and move on?

I've read a bunch of shipfics that are all happy resolutions after the confession so I wanted to try an alternative. So here is a slightly darker TwiDash fic because I am a terrible person who must make ponies suffer. Oh God Why?!

Edit: Now with addition of new cover pic used with permissions from aeroytechyon_x
Reformatted with less walls of texts and less Lavender Unicorn Syndrome as of 03/20/2015

Sequel here.

Twilight Sparkle summons Fluttershy and Pinkie over when she has a new spell that should let her see into different realities. She wants to see if there was really an endless number of possible realities. Pinkie ends up having Twilight royally mess up the spell; it gets overcharged and switches their Fluttershy for a different reality's Fluttershy.

Both Fluttershys have to adjust to their new lives, all while Twilight tries to find a way to switch them back.

Co-written by Poison Cure
Edited by Lathier

Cloud Kicker might just have the wildest life of any pony in Equestria. Marvel at the insanity that is her life, and laugh at the suffering of her poor beleaguered best friend, Blossomforth. And maybe, just maybe, there's more to her than just the lovable sex maniac everypony thinks she is.

This is a semi-sequel to "The Incredibly Dense Mind of Rainbow Dash." Not really a proper sequel, since it's focused on Cloud Kicker and Blossomforth instead of Rainbow and Pinkie, but it's in the same continuity. So I guess that makes it a follow-up-side-quel story. Or something. You don't need to have read "The Incredibly Dense Mind of Rainbow Dash" to read or enjoy this, but you ought to read it anyway, just because.

TvTropes Page

The central story of the Winningverse.

We got a tag for Cloud Kicker, but Blossomforth still deserves one too.

There is a world where Life and Death govern all imaginable realms. A world where Watchers guard over their planets and the creatures that roam them. In this world, a young soul goes on a journey to a place he never thought existed, after cutting an untold deal with Death.

Equestria, a place of magical creatures and mysteries, offers him a new chance at life. A chance he will have to pay dearly for. This is the written story of his adventures, some of the sorrows and victories of his life as he goes through great challenges and fights his inner darkness.

At the end of this journey, one begs the question: What is better? To be born good, or to overcome your evil side through great effort and sacrifice?

Tagged with Human for the prologue.

Follows show's cannon up until end of Season 2.

Now a published book!
And it's own TvTopes page!

Spanish translation: Here

First chapter published January 2012
Marked as Complete on 31st August 2014
Published (printed) on 25th November 2014

PM me for the full digital version of the now-printed book! (includes text PDF, full cover and fan art)

"My name is Rick Gärtners, and I write this diary to whomever comes across it. I am a thirty-eight year-old male with no spouse, but that's irrelevant right now. If you do happen to come across this, note for what you're about to read is a record of my life's history; day by day, month by month, and year by year. But never will you expect what's written in this forgotten journal. So sit a while, my readers, as you'll see how being shown to "kindness" can change my malevolent life... forever."

A Fluttershy rendition of 'My Little Dashie' and written out of pure inspiration of becoming a writer.

2020: Story is undergoing revision. When it'll be done is not estimated.

You, a great, famous scientist, after many years of being stuck in Equestria, find a way to return home, the only problem is that there is no way back.

Something, or someone, will try to stop you, even though it will be a benefit to everyone... Except for one pony.

Proofread by this guy.

Fluttershy finds a demon from her past, and confronts it head on with the help of Rainbow Dash, who has yet unconfessed feelings for the shy pegasus.