This story is a sequel to The Many Secret Origins of Scootaloo

When Scootaloo's attempt at flying causes her to crash into Twilight's lab, it sets off a chain reaction that causes Twilight to disappear, leaves the library in shambles and Scootaloo knocked out. A wave of purple energy rips through Equestria, leaving all to wonder 'great, what now?'

When Scootaloo awakens, she learns from the Bureau of Undoing Trouble from Twilight Sparkle that this world's Twilight is gone... and in her place are dozens of Twilights from different dimensions, tearing across the land. Worse, Nightfall Eclipse, a wicked Twilight from the antimatter universe, is assembling other bad Twilights to form The League of Evil Twilights, who seek to take over Equestria.

Now gifted with the ability to track down these Twilights, thanks to the explosion, Scootaloo will seek out these visitors from other universes in the hopes of sending them home and getting the real Twilight back.

Crisis of Infinite Twilights: Truth, Dare or Drink, the official spin-off, can be found here

Tvtropes Page can be found here

A listing of all the Twilights introduced so far (warning, SPOILERS) can be found here

Luna was never banished, Discord is Celestia's court jester, the Elements of Harmony do not exist, and Twilight grows more pompous and more egotistical every day.

Celestia is not amused.

This story is on indefinite hiatus. I might revisit it, so it's not cancelled, but I'm not currently skilled enough as an author to do some of the things I wanted. Believe me, I've got the drafts to prove it.

Twilight Sparkle has overcome many trials and tribulations, all of which have challenged and changed her. Now, as a ruler of a new demesne of Equestria, she must face the world in a new light and learn the rules to play the game.

Things are different in the world of sovereigns. Foreign rulers are not as understanding or compassionate as Princess Celestia, nor are they as forgiving. Twilight must find a balance between being an effective ruler, and a strong diplomat. But with new trials arising at every corner, can she manage to maintain herself? What sort of ruler will she become? And will she manage to protect her own little ponies?

A reclusive mage.
A devoted cleric.
A disgraced sell sword.
A beautiful thief.
A timid knight.
A travelling gypsy.

Six mares who've never met, will suddenly be thrown together as an ancient threat returns imperiling their entire world. Now these unlikely heroes must band together, or their entire world is doomed to eternal darkness.

This is a dark fantasy retelling of the series premiere, using Dungeons and Dragons 3.5 edition rules, spells, and monsters. It was an idea that I've been wanting to write for a good while, and I hope folks enjoy it.

During the battle with the changelings, a trapped Discord manages an undirected spell that reaches across universes to bring an agent of chaos to Equestria. What's brought back more than qualifies.

Steam! Gears! SCIENCE! A very confused Spark! And, eventually, really good coffee.

Here comes Agatha Heterodyne--MARE GENIUS!

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

Twilight Sparkle was presumed to be dead. Destroyed without even a body to bury, the young victim of a deadly magical surge that claimed the lives of many others along side her. More than a decade later, reports of a violent murder by a pony bearing her name are brought to Celestia and Luna's attention. A trail of carnage leading directly towards Canterlot's doorstep, brought by a pony who strikes without mercy. As Twilight approaches, in service to an unknown master, the Alicorn Sisters desperately try to uncover what happened all those years ago.

Edited by Zintegy and The Pink Mugsy

Chapter Heading Art by KirillK
All Sketches and Artworks can be found HERE

King Sombra’s dark influence was obliterated by the Crystal Heart, and the villain is well and truly dead. But when he attempts to steal the afterlife of an innocent victim, a human spirit is left hurtling towards Equestria, where this unfortunate soul is revived into the only vessel available: the reconstituted body of King Sombra himself.

Thus, a cheerfully oblivious alien is crammed into the form of the most evil and malicious being Equestria has ever known. Not that Shining Armor and Cadence know this, of course. As far as they are concerned, the King is back and he’s lost his fricking mind.

Click here for the TV Tropes page!

During a lull in the conversation at an upper class charity dinner, Rarity takes a moment to contemplate some commonly held assumptions made of Princess Celestia. Specifically, her table manners.

This is a fic based on the Time Loop Files, the format of which was first codified by Innortal on fanfiction.net.
Here's a brief guide.
The basic idea is, one character (the Anchor, usually the main character of a fictional setting) is looping back to the very first moments of their parent series every time either they die or some kind of time limit expires. They of course end up monumentally stir crazy given enough time.
Eventually others start to loop as well.
The reset is not always perfect. Sometimes a loop's history will be different to the "prime" loop, or canonical plot.
"Crossover" or "Fusion" loops also occur, randomly. These can involve the home loopers having a guest, or the anchor for one universe spending time in another, or replacements of one character by another.
Vacation Loops are where the Anchor (or others) decide/s "buck it" and lets off steam by doing whatever comes to mind. There's little or no attempt to maintain the original timeline.

In addition, and particularly more recently, it should be known that this story has a collaborative element to it - people may submit loop ideas or loops, ideally at the Spacebattles thread (a link to the current version of which is on the Trope page), and they may become included.

There's two page image options, thanks to Filraen - the current page image has been edited by the original creator from this work of theirs.. The other one is here:
http://hourglass-vectors.deviantart.com/art/MLP-Loops-466030169