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.

Recently rewritten. Contains occasional adult humor and violence.
***
On a request from Princess Celestia, Twilight Sparkle and the rest of the mane six explore an abandoned mansion located deep in the woods. While doing so, they unwittingly stumble across an enchanted mirror that scrambles their DNA and pops out three brand new bouncing baby ponies. Hilarity and drama ensue as the mane six must cope with being suddenly thrust into motherhood, as well as protect their new foals from a dark god that wishes to use them for his own sinister gain.

***

Fanart:
The three foals. by Freefraq on Deviantart.

After an unknown accident Twilight Sparkle and Rainbow Dash awake to find themselves sharing the same body! Now they must struggle to hold themselves together as their world is turned upside down. How long can two ponies exist in a single mind? It’s a race against time as they search for answers before it’s too late. When all is said and done, you’ll never look at Twilight Dash the same way again.

The Princesses find an alien creature barely clinging to life at the scene of a terrifying crash. Can the Combined Power of the Elements of Harmony save it, or more importantly, should they save it? Will the arrival of this strange creature tear Equestria apart?

TV Tropes
https://tvtropes.org/pmwiki/pmwiki.php/FanFic/Article2

Celestia and Luna were born as unassuming foals in troubled times. But already marked for greatness, the simple earth ponies stand to face a world set against them, full of danger, fear, and sadness. A world they will change forever.

A sweeping epic taking place before Equestria was made, where Celestia and Luna must rise from normal foals to become the Princesses we know them as, beset from all sides by monsters, other ponies, and even the forces that govern nature. Their tale is as tragic as it is triumphant.

Currently on hiatus. For more info, go here.

(Cover and internal art by Madmax)
(Editing credit predominantly Lightside Luc)

It's just another normal day in Ponyville. Pinkie's tending to Sweet Apple Acres, and Rarity's got the weather under control. Fluttershy's anxiously planning for a big bash the next day, while Applejack works her latest fashion line for Hoity Toity. And Rainbow Dash is preparing to shelter several critters from the Everfree Forest from a rampaging cockatrice.

Absolutely nothing can go wrong.

Celestia wants Twilight and her friends to loosen up a little bit around her. Luna just wants to try the hard cider. During a surprise visit to Sweet Apple Acres at the tail end of cider season, Princess Luna has just a bit too much to drink, and when she makes a rather inappropriate joke, Twilight comes to the very uncomfortable realization that she has never seen Celestia excuse herself to use the restroom.