After discovering that Cadence is not who she appears to be, Twilight is sent to another world entirely by the disguised Changeling Queen to avoid her plan being disrupted.
When Twilight lands, she discovers that not only have Spike, Owlowiscious and Peewee followed her, but that they've arrived in a world where the main sentient species is human.
There's still a place where they teach magic, though.
Crossover with Harry Potter. Twilight will be effectively taking the role of Hermione.

I've marked this story as cancelled to reflect the unlikelihood of it continuing. If I do come back to it I'll revert that.

Fancy Pants and his lovely wife Fleur are quite possibly Canterlot's most heroic duet. Together they conquered countless events, faced hordes of snobbish socialites, and emerged victorious from the most dire of faux pas. May their bravery and finesse be forever remembered on parties to come!

There is a missing element in their perfect life, though: the joy of having a child and becoming a family. When conventional methods fail, will the couple muster enough courage to seek out the alternative, or will they stay a duet forever?

Enter Chestnut—a daring filly from beyond Equestria, out of their social stratum, and definitely exceeding their boldest expectations.

For better or worse.

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 But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.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

After the most important night of her career is ruined and its saboteurs not even so much as punished, Octavia's life changes. She begins to pursue a path that has never been seen before in Canterlot, where concertos and rhapsodies give way to controversy and rebellion.

A path where symphonies are composed with cans of spray paint.

Cover art used with permission by LuGiAdriel14

Over a thousand years ago, two royal siblings fought for the sky and were exiled, one by her sister's hoof, and one in penance for what she had done.

In the present Republic of Equestria, no one remembers them as anything more than legends and old pony tales. Save for one shy filly who fell from the sky one fine summer's day.

An Alternate Universe "What If" tale, reconstructing the beginning from a different angle.

This story is a sequel to So...What Now?

Scootaloo. Everypony in Ponyville thinks she's an orphan. All she does is ride her scooter around town, get in trouble with her friends, and then disappear whenever nothing's going on.

Scootaloo. Everypony in Ponyville thinks she's an orphan.

But she's not.

And now, her secrets will be revealed...

(A sidestory to "So...What Now?".)

Celestia had a problem. Somepony wrote a novel about Nightmare Moon's rebellion. This made Luna quite unhappy, and unfortunately for her sister, Luna has not yet gotten the hang of modern traditions like freedom of speech, the abolition of the death penalty, and not bothering Princess Celestia when she's trying to sleep.

Fortunately, Celestia also had a faithful student, one who is now a Princess with an ill-defined portfolio and perfectly capable of dispensing justice by the laws of both today and one thousand years ago.

Now Twilight Sparkle has a problem.

(Title image hacked together from vectors by Martinnus1, Hawk9mm, and Paulie15.)

This story is a sequel to The Other Jake

Shortly after being forced to confront numerous personal demons, life complicates further for Skitch-Sketch when a UFO (unguided falling object) crashes at Sweet Apple Acres.

Weeks after that, it's time to return that object to its owner, the mysterious Jacoby Flynn, and decide if the world outside of Equestria is any more accommodating than Equestria is outside of Ponyville.

Another story in the Skitchverse.

Brought to you by Loyal2Luna, this new Downloadable Content for Mass Effect 2 brings the fight to Equestria.

Just about ready to embark on their mission to stop the Collectors from further abducting human colonies, Commander Shepard and the crew of the Normandy SR-2 are given a new priority, when the Illusive Man tasks them with investigating the mysterious disappearance of a Cerberus science team.

Soon, what begins as a simple search-and-rescue unveils a mystery millions of years in the making, and the Commander finds himself thrust into a situation he couldn't possibly have prepared himself for.

Join the Hero of the Citadel as he uncovers the secrets, combats the demons, and ultimately decides the fate of the impossible world known as "Equestria."

A.K. Yearly's epic continuation of Daring Do is coming up. While fans eagerly await the next installment of the series, Yearly's publishers eagerly anticipate the estimated profit.

So what happens when they find out everything was real?

Picture by Austiniousi