Twilight Sparkle broke time when she got her cutie mark. Now Twilight and Sparkle are sisters from another time. Twilight is hailed as the potentially greatest light magician of all time, and already has a reputation as a hero by the time she goes to Ponyville. This isn't her story, not primarily.

Sparkle is an orphan - her dark magic killed her parents. She lives with her brother in Canterlot's industrial sector because they can't afford anything better. She can't leave either. She's a natural dark mage; while Sparkle won't go mad like Sombra, her reputation is hardly any better. Worse, the law doesn't see her as a good pony.

The fact that the dead don't stay dead around her, or that Thorn - Spike's double - is an undead, soul-eating abomination, are other matters altogether.

(Also has some Slice-of-Life, but fimfiction tags won't let me put it with Adventure.)

Has an ask blog to go with it: Ask Sparkle and Thorn.
Also has a TvTropes page: Split Second Tropes.

Featured on EQD.

Cover art by Swirling Line.

This story is a sequel to Kingdom Hearts F.I.M: Rise of The Elements

Can be read independently of that story, however.

Spike is an orphan who's hated and ostracized for being different. Fed up with the people of his home, Spike decides to leave in order to find a place where he's accepted. However, the day before he's set to leave, Spike comes across a certain lonely girl who will change his destiny forever.

Travel back 10 years from the start of Rise of the Elements and experience the very beginning of Spike's adventures with Twilight and the others. Discover the truth of Spike's origins as he struggles to understand what having a family really means.

This story is a sequel to Kingdom Hearts F.I.M: Days Long Past

Can be read independently of that, however.

Six Years have passed for Twilight and her friends since the death of their home world as well as Spike's disappearance. Six years have passed since Master Luna took them under her wings in order to teach them how to use the one weapon that may help them save Spike: The Keyblade. Now, after those long years of training, these friends are ready to see new worlds, fight new enemies, and save old friends. Limits will be tested, and bonds will be broken.

Will their friendship be enough to bring Spike out of the Darkness?

Kingdom Hearts based MLP story, no Sora, and no need to have played the games. Characters are human, but those who were pegasi in the show still have magic wings, just as those who were earth and unicorns still have unnatural strength and magic, respectively.

Now with a Web Comic! Hosted on Tumblr DeviantArt Taptastic, and my user page!

One day, Equestria stopped being in one piece, and started being in a million pieces. The world literally ended. Life didn't. Any way they could, and any way they had to, ponies survived in the debris of Equestria.

On one piece of Ponyville, they survived quite well. Key Stone grew up with a simple but comfortable life. He spends all his time staring at the sky and buried in books, waiting for the faintest hint that life is out there.

And then it arrives.

Story returning to updates soon!

Set 100 years after the war with the zebras violently ended, this is the story of an unlucky trader who suddenly finds himself dead and his afterlife somehow tied to two strange ponies. He now has to try and figure out daunting questions such as:
Who are these ponies?
Why is he stuck following them?
How did this happened?
Where are his hooves!?

This fan-fic is just a third of a much larger story...
-Hear another side of the larger narrative with Fallout Equestria: Sounds.
-See the bigger picture, take a look at Fallout Equestria: Sights.
-Follow the progress of all three tales at the Sights Sounds Souls Tumblr(and ask Colt questions).
-See all the parts in one place at the Project Hub.

Scootaloo ends up with her father's lunch by mistake. Reality is almost destroyed in the process.

A collaboration with RainbowBob.
Now featured on Equestria Daily!

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

This story is a sequel to Spiders and Magic: Rise of Spider-Mane

Officially Complete!

A collaboration done with Azu.

With the Green Goblin defeated, Peter Parker and Twilight Sparkle are ready to take on their greatest challenge yet: parenthood. They have eleven months to prepare. In the meantime, they’ll also have to earn the trust back of everypony in Equestria, survive Twilight’s hormonal outbursts, deal with Black Cat’s antics, endure Trixie’s sarcasm, and work up the courage to take the next important step in their lives.

Cover image done by Black Freya

This story is a sequel to Spiders and Magic II: Eleven Months

Officially complete!

During a time of peace, Peter disappears in what seems to be an accident and is pronounced dead. However, he wakes up in a distant future where Equestria is in ruins, most of his loved ones are either dead or captured, and the world is under the rule of Empress Chrysalis. Spider-Mane must reunite with what remains of his friends to save this tattered future, all while desperately searching for a way to return to his original timeline.

*Thanks to Kestrel, Darth Cygnus, Commander Stelios, Regreme, Vandenbz, Lord Lycaon, The Slending Angel, cosmic flash, Derp McShirk, NeilHD, and Dark Seqvus, for editing!

Collab with Azu
Cover art done by JinZhan

Featured: 2/28/2015 -3/2/2015 (Thanks, everyone!)

This story is a sequel to Stallions of Harmony - Longest Night

Life wasn't easy for Thunderlane. Since losing his parents, his life was reduced to work, caring for his little brother, work, dealing with Rainbow Dash, work, his questionable relationship with Blossomforth, work and even more Rainbow Dash. Not even Nightmare Moon's Everlasting Night changed that.

Just when it seemed like it won't end, his life was hit by a certain Lightning...

--
Other tag stands for Blossomforth (who has no tag), Cloud Kicker and Raindrops (who both have, but there's a limit).