This is the story of the end. This is the story of the death of Equestria. It is the story of the reign of her royal majesty, Princess Twilight Sparkle of the Fading Sun.

The alicorn sisters are dead and Equestria has turned to Twilight Sparkle to guide it. However, just maintaining a dim sun a fraction as bright as her mentor's keeps the new princess near her limits.

Years have passed and Twilight Sparkle is sure of only one thing. Equestria is dying.

NOTE: Written before "It's about Time" in season 2. Everything after "Read it and Weep" was ignored throughout this story.

Worlds begin to collide when Applejack discovers a strange creature from another world and quickly makes him apart of the Apple Family, naming him Johnny Appleseed. But as Johnny grows up he quickly notices the differences between him and his adopted family and seeks to learn about his true parents, where he came from and who he really is.

This is a collab story that I have written alongside lyra_lover777. Also the events of Equestria Girls never happened in this universe.

Cover Art done by Eveyann

Scootaloo wants to be just like Rainbow Dash, and barring that, to be like every other pony. She's ashamed of her true nature, the one she must hide from everypony or be hated and cast out, or worse. She doesn't know what she is, only that she can't eat the same way other ponies do, and she has to keep the terrible consequences when she feeds too much always hidden and never seen. But when a pony begins to truly care about her well-being, Scootaloo finds out that being loved makes it harder to keep a secret than when nopony cares about you at all.

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

Early twentieth century strongman Arthur Saxon is summoned to Equestria to save the country from Tirek's return.

Exactly what it says on the tin. Not much else to be said.

Due to an editing/publishing error, all of Twilight's friends have now 'officially' died of old age. This leaves an immortal Twilight to grieve over the tragedy of how she outlived all of her friends and will continue to do so for the rest of her eternal life.

Seeing the obvious pain that this news is having on Twilight, Princess Celestia moves to console her with the help of her supposedly-but-actually-not-really-deceased friends.

Cover image belongs to Shawnyall.

Ebola-chan stops by for a visit to Equestria on her journey across the world.

This story is a sequel to An Affliction of the Heart: Volume Four

With her newfound responsibilities as Queen, Kuno has seen fit to lead the changelings towards a life of coexistance with ponies.

But there are those who would wish to see such an endeavour fail, and they're not above taking action to make it fail.

Cover art commissioned by Iakovl, drawn by Derpah.

This story is a sequel to Thrown Abroad

After the events of Thrown Abroad, Suncloak the changeling is happily living in Ponyville. Well, sort of. He needs the love of friendship to stay alive! Luckily, there's plenty of ponies who would want to be friends with him. But let's not forget about other changelings here...

You know, this would be a lot easier if the whole concept of friendship wasn't so needlessly difficult.

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Amazing cover art by Wolfeh! Find her Tumblr here!
Fanart!
To be found on Equestria Daily here!