Fluttershy was beginning to worry why everypony was acting like she wasn’t there—more so than usual—until she discovered that despite spending most of the day in Ponyville, she’d never even gotten out of bed. At least, her body hadn’t... Nor was it breathing...

Even if Fluttershy isn’t ready to give up on life just yet, The AfterLife is calling, and it isn’t patient.

Written by Chaotic Dreams and GaruuSpike.

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.

After the Changeling invasion, Celestia and Luna make the decision to have Twilight investigate the Elements of Harmony and solve the mystery of their power.

A thousand years later, Rainbow Dash awakens in a world she does not recognize. She has no idea how or why she came to be there. She does not know the language, the geography or any of the rules of this new time. She soon finds allies in Star Fall, a scholarly pegasus whose Talent is Magic, and Astrid, Star Fall's Griffin guardian. Together they set out to discover why Dash has been sent to the future, and how she might return to when she belongs.

War threatens the nations, a Nightmare stalks the shadows, and Rainbow Dash's arrival has turned her into a wild card in a deadly game that pits the law on both sides of a broken Equestria against a mysterious criminal figure, Max Cash. Yet the stakes are higher than anyone knows, for in her research Twilight Sparkle discovered a dark secret about the Elements, something that will shake the foundations of the world.

Cover image by SierraEx
Has a TvTropes page

On secret assignment from Princess Celestia herself, Twilight investigates a powerful magical artifact for clues to the mystery of Luna's transformation in the evil Nightmare Moon. Incautious use of the artifact sends Twilight hurtling back in time. Can Twilight discover what caused Luna's transformation? And will she ever make it home again?

Kickass cover art used with permission from Bitz.
http://allthebitz.tumblr.com/

Harry Dresden, Chicago's only professional wizard, accidentally travels to Equestria after being attacked in the Nevernever. Twilight is none too amused with their newest 'guest', but trouble is brewing. Somepony is planning something sinister and the mane six may need Dresden's help however little some of them want it.

Story Image by: Lynxgriffin
Cover arrangement by: Novel Idea

While researching the properties of light, Twilight realizes that she might be able to unlock the secrets of invisibility. However, being invisible has its consequences. She will soon learn that losing the ability to see oneself is a great way to lose one's mind.

(a loose adaptation of The Invisible Man by H.G. Wells)

~~~
my first published story, so feel free to tear it apart.

After a summoning mishap, six champions from Runeterra's League of Legends arrive in Equestria. At first, they are focused entirely on getting home, but soon find out that it might be more complicated than they thought when Discord decides that he can use them for his own ends. Continued in The Redemption of Jericho Swain

We all know the story of how the Princess’ young student and five friends defeated Nightmare Moon and brought Princess Luna back to our lands. But what if the tale were false? What if the young Twilight Sparkle on the event of her entrance exam had not been rescued by Princess Celestia, but instead lost her mind among the power of her youthful surge and had to be sent away, far away before she could destroy all of Canterlot with her newfound power. Now the feral unicorn prowling the Everfree Forest only vaguely remembers her past, slipping away from constant terrifying attempts to capture her.

And she is beginning to remember what true power felt like.

Editors include: Peter, Justin, Featherprop, Mitch H, and Bad Horse
Featured on Equestria Daily
Reviewed by Chris on One Man's Pony Ramblings and by Paul Asaran on his review blog
Now with a TV Tropes page

Physical books are available on Lulu.com
Monster in the Twilight (Paperback) 272 pages
Monster in the Twilight (Hardback)

"It's so nice to see you again!" said the thing that was not Celestia. "Oh yes, I know who you are, Twilight Sparkle. I had a taste of your magic the first time we met. Mortals forget things so easily, I find. Allow me to refresh your memory: you tried to kill me. But you failed, Twilight Sparkle. You only mostly killed me. And I guess that makes you one very unlucky little pony."

This story is a sequel to Lines and Webs

For four long years, Celestia's apprentice Twilight Sparkle, once a model pony and a hero among heroes, has waged a bitter and secret struggle with her onetime mentor. Though she works from the shadows, directing her forces from the Old Capitol in the Everfree Forest, Twilight Sparkle is unable to gain any advantage,

Likewise, Princess Celestia finds her once-faithful student far more cunning and elusive than she had anticipated, and even now searches for a way to bring Twilight Sparkle's rebellion to its knees.

It is a game of greys, of knives in the dark and of poisoned wine, where pawns are moved and traded and exchanged for greater advantage, all the while drawing both sides nearer to the conflict which shall tear Equestria in two.

At the center of this conflict is a new pawn, one who only wished to see the truth for herself. Drawn into a deadly game whose rules she does not understand, Sweetie Belle must learn to survive in a world where all is darkened, and nopony can be completely trusted.

Because when gods play chess, all pieces are expendable.

A nation will crumble, old enemies shall return in the most unexpected ways, and regardless of who is victorious, only one thing can be certain.

Nothing shall ever be the same.

Followed by Stormsinger.