When Ruby boards the first trans-oceanic flight in Equestrian history, the last place she expects to end up is stranded in the middle of Eternity's Crossing in the wake of a horrific zeppelin crash. After a mysterious tower leads her and a fellow survivor to discover a twisted and fragmented city twenty thousand feet below the surface of the ocean, though, a bit of fire and smoke is the last thing she needs to worry about. Between the horrendously disfigured residents and the paranoia of the madmare who once built and controlled it, daily survival in this corrupted utopia is anything but a guarantee. But with the help of some new friends and a few genetic enhancements, Ruby isn't going down without a fight, and in the process might just discover that the deadliest weapon in Harmony is herself.

An adaptation of BioShock for the world of MLP. Written to be comprehensible to anyone, regardless of whether they've played the original game.

Being a changeling has its benefits, but when a changeling leaves the nest to live a normal life away from the tyranny of the queen, how long can he keep his secret in a world where he is hated? How long can one pretend to be somepony they aren't?

Kuno, a young changeling, is left weak, bloodied, and bruised after the events of the Canterlot wedding. She is soon discovered by Warden, a Royal Guard. But for some reason, Warden shows her mercy. Instead of taking her into the custody of the Royal Guard, he becomes both her captor and her savior. But over time, Kuno will come to ask herself the hardest question she has ever pondered: Can a changeling feel love?

In a freak accident from the Cloudsdale weather control team, Twilight is struck down by an errant lightning bolt. But the veil of death is relatively thin...

A single changeling is blamed for making Chrysalis' plan to take over Equestria fail. He's banished and thrown out of the hive, ending up somewhere far away.

Luckily, he ends up not too far from a certain well-known village, where he can feed to his heart's content.

Needless to say, not everything goes according to plan.

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Now with a French version, courtesy of Wansdich, here.
Fanart! Check it out here. And even more here!
Now in ereader-friendly PDF version, by Starflower Hooves! You can view and download it here.
Featured on Equestria Daily!

In the year 2148, Earth Ponies discovered they were not alone in the universe.

Discovering an ancient cache of technology belonging to an extinct race identified only as the Alicorn, the Earth Ponies soared to new heights of technological advancement. With their newfound strength, they searched the galaxy for more hidden treasures of the Alicorn empire, soon discovering the existence of other space-faring races that shared their lust for progress and knowledge.

But when their fevered searching unearths ghosts that were better left buried, and mysteries better left unsolved, the Equestrian Galaxy is besieged by an ancient foe bent on nothing than the total destruction of life. Only one group of friends, led by a single Earth Pony soldier, can stop the coming darkness, all the while trying to answer the great question at the center of it all; what happened to the Alicorn Civilization and the Equestria that was?

A story lovingly ripped off from the Futurama episode of the same name.

Twilight gathers the girls to her basement to reveal her latest invention. Unfortunately, they get distracted by another of her inventions: the 'What If" machine, a device capable of answering any 'what if' question posed to it. Follow along as the mane six discover the improbable scenarios that could have been their lives.

The Metro tunnels of Stalliongrad shelter the last remnants of ponykind from the ravages of the Apocalypse. Beneath the earth, ponies struggle to survive against mutants, radiation, and each other. But when an unstoppable threat emerges from the darkness of the Metro, one pony must brave the shadows to save not just his home, but the very existence of his people.

Waking up with a hole in the head might seem like a bad way to start your life, but what if you deserved it?

"Every pony like me should be shot in the head at least once."

When he discovers the entire wasteland hates him, the amnesiac Ripple, once Two-Kick Rip the raider warlord, sees his wounds in a very new light. On a path that's half vengeance and half bid to redeem himself, he must rid the wasteland of his old gang and another, much more sinister foe.

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The cancelled sequel is over at Fallout Equestria: Echoes of Chaos.
This fanfiction is based on Fallout Equestria by Kkat; a familiarity with the source material may aid your enjoyment.

Coin Slot, a slaver in the Equestrian Wasteland, is making just a regular sale when something a few miles away explodes violently. Deciding to check it out, she discovers a strange weapon of unknown origin that seems to mesmerize its targets. There are... drawbacks to this weapon, however, and its discovery soon leads Coin down a chain of events that will change her morals, lifestyle, and even her very soul... provided that she manages to survive. Will the friends she makes be enough to convince her that her slaving ways are immoral? Or will they just reinforce the belief that that is one of the best ways to survive After the End?

A side story of Kkat's Fallout Equestria. Which is excellent.

Here's a link to the Gdoc's index

Cover image by http://felixattchar.deviantart.com/. He's awesome. Look at his stuff.