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.

I've spent the majority of my life tilling the desolate land in which I live. Every day, I wake up to move useless rocks from one location to another. This is an archaic line of work that my family has clung to for generations. It is a dull, grey existence.

Today, I have woken up in a strange room, lying in a bed that isn't mine. I'm surrounded by five mares whom I've never seen in my life. They claim to be my friends, and expect me to bring joy to the hearts of everypony.

Joy? I don't think I've ever experienced this for myself, so how am I supposed to thrust it upon others?

My name is Pinkamena Diane Pie, and I'm not sure what to make of this situation.

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?

Twilight is now gone, her friends and family are devastated. Twilight must now have to find a way back. She has to. Doesn't she?

Special Thanks:
Thanks to Stormy Venture for all the help!
Thanks to The Myth for the plot!