This story is a sequel to Doctor Whooves Episode 1: The Doctor in the Box

Following an accident with the TARDIS, the Doctor and Twilight find themselves 1000 years in the future. Here they find a futuristic Equestria, a confused Queen Celestia, and a pony from the Doctor and Twilight's future who wants revenge.

King Sombra wants his old empire back, but he's become weak and needs to feed. He looks for help, and what he does is unexpected. He finds Princess Luna and re-corrupts her to return to Nightmare Moon, brakes Discord from his stone prison, gives Trixie back the alicorn amulet, and finds Queen Chrysalis and her changelings. They go to take back The Crystal Empire as a team. This is so the six friends can't stop all of them together. After they take back Sombra's Empire they decide to take all of Equestria, and what happens will make all of Equestria's history change.
Big Thanks to nygiants93 and OctavianRex

Nightmare Moon, Discord AND Crysalis have returned to exact their vengeance on the six little ponies that caused them so much grief. But they aren't going to fight them themselves, what fun is there in that. So they decided to send them to a suspended reality where they can pit Twilight, FLuttershy, Pinkie Pie, Rainbow Dash, Rarity and Applejack against some of the greatest fighters and monsters ever invented in bloodthirsty duels to the death. Will anypony survive?

This story is a sequel to The Shadowed Nightmare

The Elements of Disharmony have been discovered. As they choose their new masters, it is a race against time to find the wielders before they discover their Elements, or the safe streets of Canterlot will erupt into a full-blown war between the masters of Harmony and Disharmony. However, it will not be that simple. Somepony is working behind the scenes; somepony is pulling at the strings of the Elements of Harmony and Disharmony alike. Who is this certain somepony? Twilight Sparkle is summoned to Canterlot to find out, where Princess Luna and a group of scholars are studying the Elements that they have found.

A storm is coming to Equestria...a storm that, when it hits, could destroy everything in its path.

Sequel to The Shadowed Nightmare. If you have not read that, what happened in that story should become apparent as you read this one--though if you want to go read it, by all means go ahead. My personal/"ponysona" OC will not be a character in this story, although this story includes the original villains The Shadow and Puzzle Master from The Shadowed Nightmare.

UPDATE December 12, 2012: New chapters (which is to say Chapter 6 on) will feature cover art by Youkaiyami.
UPDATE May 6, 2013 (Geez, I've been working on this for a long time...but don't worry; I haven't abandoned it): Yeeaah, it's been a few months since I've seen any activity from Youkaiyami, so....welp. So much for the whole cover art thing. :( ah well.
UPDATE May 13, 2013: Next chapter will be released May 27, and from then on new chapters will be added much more often.
UPDATE November 29, 2013: The final chapter will be released at the end of next week at the absolute latest. Also, since I am going to submit this story to EqD, I will be revising some of the earlier chapters to fix some basic writing mistakes and flesh out the scenes with better descriptive imagery.

UPDATE February 18, 2024: Haha, okay, so it turns out that I may have slightly overpromised when I wrote the previous update a decade ago. Best I can do for now is quote Douglas Adams: “I love deadlines. I love the whooshing noise they make as they go by!” I plan to finish on chapter 20. Hopefully this time I can make the wait a little shorter.

Big Macintosh goes on strike when he sees he's the one doing all the heavy lifting and harder work at Sweet Apple Acres while his sisters frolic. His idea catches fire throughout Ponyville, and soon every stallion is up in arms! Sexism explodes in the tiny town, it's Stallions on Strike!

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
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Asylum Fan Group
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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 Past Sins

Side-story to Past Sins - Spike almost lost Twilight to a hangmare's noose, but now Twilight is safe and Nyx is a filly again. Normal life is returning. Still, Spike can't ignore the fact that Nyx just isn't the same as he remembers her. Her temper is more volatile, and, when she gets angry, all he can see is the rage-driven Nightmare Moon of legend.

And thus Spike has to wonder: Is Nyx truly reformed, or is she one bad tantrum away from calling herself Nightmare Moon again?

This story is a sequel to Past Sins

Side-story to Past Sins - Slowly, the wounds inflicted by Nightmare Moon's reign heal. Ponyville is being reconstructed, and the last refugees are leaving the castle. Nyx is with Twilight. Celestia and Luna rule Equestria and guide the sun and moon once more. Everything is as it should be.

But some things are never washed away. These are the things that remain to remind us of the past. They remind us of the good times we've had with friends and family. They never let us forget the mistakes we've made. Everyone has them. Twilight has them. Nyx has them.

And, on occasion, when you share your scars, your photos, and your trinkets with another, they just might share theirs in return.

This story is a sequel to Past Sins

Hearth's Warming is a time for friends and family to come together, celebrate harmony, and welcome the new year. Nyx is looking forward to just this as she rides the train to Canterlot with Spike and Twilight. She's going to meet her extended family for the first time and wants nothing more than to make a good impression. Yet, the sheen of the holidays can't hide the trouble caused by meddling grandparents, relentless reporters, and a paranoid uncle.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?