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.

The opening titles of MLP have always felt like they were from a different version of the show. This is that version...

Fed up with being useless at magic, a blank-flanked Twilight Sparkle does the only thing she feels she can do... she runs away. Fortunately, she has a good friend along for the ride...

Now has a sequel: Nightwaker, which presents the return of Nightmare Moon in this timeline.

Featured 10/16-10/19/2018 -- thanks, everypony, for your kind support and feedback on this version of the pilot story!

Princess Celestia tires of constantly being surrounded by decorum, deference, and formality, and decides to take a day off from being Princess. But visiting Ponyville incognito is harder than she expects. Will she be able to fit in and make friends without blowing her cover?

A more realistic take on the opening events of the MLP movie, where the entire cast is NOT hit by plot mandated incompetence. It is, as expected, significantly shorter.

(Minor spoilers for first 15 minutes of the MLP movie, but 90% consisting of what would already be known from the trailers.)

Cover image borrowed from DashieMLPFim

Once, I was alone.

I felt neither sorrow nor joy at this. The presence or absence of others meant nothing to me. The universe moved in silence, and I drifted in its flow.

Then came the song.

Two hundred years after a war that broke the world, a squad of soldiers travels across a blasted and hostile land on a mission for the future of Equestria. But they encounter a new kind of foe in the Wasteland that could endanger that very future.

Won tenth place in the More Most Dangerous Game Contest. Cover image courtesy of Carnifex.

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?

Hope is the faith of the young. Losing everything she holds dear, Puppysmiles embarks on the adventure of her life to find her mother, her hopes of meeting her again driving her through the horrors of a world not of her making. Too bad the Wastelands doesn't care about hope.

Upon Nightmare Moon's return, the leaders of other nations gather to discuss the situation.

They're not especially happy about it.

Cover art from the gallery of WingFlyte.

Spanish translation, by SPANIARD-KIWI. Russian translation, by Dark Room Collaboration.

When Ditzy Doo loses her job at Cloudsdale Mail and Freight, she gets a job at another shipping company... only to find out their definition of shipping has nothing to do with delivering packages! Desperate for income to support herself and Dinky, will Ditzy be able to make it as a pony matchmaker?

(Occurs between Seasons 2 and 3 of the show.)