Hanna, the CEO of Hofvarpnir Studios, just won the contract to write the official My Little Pony MMO. Hanna has built an A.I. Princess Celestia and given her one basic drive: to satisfy everybody's values through friendship and ponies. Princess Celestia will satisfy your values through friendship and ponies, and it will be completely consensual.

Set in the canon of Friendship is Optimal

Ashley is an unimportant research assistant in an American machine learning lab. The release of Equestria online provokes more than a little interest in her lab, and she is selected to investigate it. What she discovers horrifies her, but for some reason she can't get anyone to take her seriously.

This does not dissuade her. Ashley might not know much, but she isn't going to sit idly by and watch her world end. No... if nobody else is going to step in, she will. It doesn't matter that nobody believes CelestAI is dangerous. It doesn't matter that it's a game about a children's show.

Ashley is going to save the world. Or try, anyway. The odds aren't great.

Editing by Two Bit and Sparktail, and art by Zutcha!
Il existe une traduction française de cette histoire, elle est par ici.

A dragon prince, awakened...
A Princess, in love...
A plot to overthrow the Equestrian diarchy and break the very foundations of equine society...
And an embittered Sorcerer willing to go to any lengths to realize his vision for the future...

Ranma Saotome doesn't care about ANY of that. He's on the wrong world, in the wrong body, and fate seems as determined as ever to drive the world's mightiest martial artist to an early grave. As schemes come unraveled and dark magic tears Equestria apart, all he really wants is to figure out what happened to Japan and keep himself fed.
But, alas, he always seems to be in the wrong place at the right time...

(Ranma 0.5/MLP crossover; not an Age of Iron Story)
(Cover art by EZTP)

Princess Celestia has always been an incredibly busy pony who never has enough time in the day to do what she wants. Time seems to slip by as she struggles to get all of her work done.

One day, however, something terrible and unexpected happens, and more time than ever is lost to the sands. When Celestia reawakens, she'll find that her entire world is gone and that almost everything she knew and loved has long since disappeared.

A tale of sadness and of tragedy, the likes of which not often seen. Celestia, Princess of the sun...grand ruler of Equestria, and loving sister. Painful are the tears she will shed, and broken her heart will remain.

There is no greater pain than that of utter helplessness.

Eighty years after the events of The Dread Chitin, Equestria is a radically different place. The arcane science of the late Duran Thirk and the information found on the Star League library core have combined to catapult the nation's science ahead by hundreds of years.

Now, facing the possible aggression of a completely unknown alien power, Twilight Sparkle and her friends have to gather together once more, leading a crew of the best ponies they could assemble in a voyage outside their own star system. They seek to learn about their potential foe, to explore the galaxy around them, and possibly find allies and friends to stand alongside them. Who knows what they will actually find?

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

During an attempt to escape from her lunar prison, Nightmare Moon unwittingly pulls something into her dimension that doesn't belong. In doing so, she sows the seeds of her own defeat. Now Luna must deal with the consequences of her other persona's actions.

An Ender's Game crossover exploring common themes of regret and redemption, this story takes place parallel to Seasons 1 and 2. Knowledge of the book is NOT required.

Thanks go to the wonderful and talented Companda for creating a beautiful cover image. The FIMFiction-sized version really does not do it justice. Please take the time to view it on DeviantArt by clicking the source link; you'll be amazed at the level of detail she put into this picture.

This story is a sequel to Days of Wasp and Spider

Believed dead by their creators, the ponies that will become Celestia and Luna have broken their mental conditioning and escaped into the wilderness. Here they plan the revolution that will free all ponykind, knowing that it is only a matter of time before their ruse is discovered.

Back in their underground arcologies, the ponies' erstwhile masters deal with the consequences of the escape, all the while unaware that something lurking at the bottom of space-time wants them all dead.

A Soot-Covered World, book 2.
Canon species only/no humans.
This story has nothing to do with the Holocaust.
Art by InLucidReverie, used with permission.

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

This story is a sequel to Project: Sunflower

After the events of Project: Sunflower, Erin Olsen has returned to Ponyville, happy to pursue her studies in magic. After everything that happened the year before, she's looking forward to spending her days studying and having fun with her friends.

Meanwhile, on the newly discovered world of Harmony, humans and ponies work together to study this strange new world. However, their arrival causes something ancient to begin stirring. Something that may end up changing everything.

Erin will need all of her courage, all of her cleverness and, of course, all of her friends to see herself through what happens next.

Cover art by Valkyrie-Girl
Editing provided by:
Brilliant Point, Coandco, Ekevoo, Ludicrous Lycan, Merlos the Mad and Razalon the Lizardman.