This is going to get a rewrite as a separate upload due to a complete rework and rating change. Please consider that canon to the sequel once it's posted.

Expand for more info, sequel, reading, TV Tropes page, Tumblr blogs etc.

The Elements of Harmony are only able to be wielded by a select few ponies, with little information on them through the pages of literature.

In a desperate, insane desire to search for the biological process that distinguishes a normal pony from one with the proper qualities, Twilight Sparkle resorts to restraining, analyzing, and destroying the holders of those qualities for her research. All for - according to Twilight - a purpose of "preserving the future".

But how far will her desire to research and preserve Harmony go, and what, precisely, does Twilight plan to achieve as her ultimate goal? For it is a goal that she strives to achieve—whatever the cost.

Sequel: Empress of Harmony (can be read as a stand-alone.)

TV Tropes page.
Fanfic reading done by thegibbie88
Fanfic trailer by IAmInHurt.
Musical-fic version by lazerbem

Empress Twilight
The P.A.T.H. (Ponies Against Total Harmony)
Harmony's Students
Broken and Dead Fluttershy

Vargy: Just read it and I must say, I'm impressed at how this fic evolved from something were gore was the main objective to a fic with an extremely well done plot. There's also the fact that from the beginning of this fic to now, your writing has improved tremendously! It's a pleasure to read a grimdark-gore that is so well written. This is at least how I see it.
FanOfMostEverything: …Anyway, this continues to be one of the most exquisitely horrifying stories on the site. I look forward to Twilight's inevitable comeuppance…In any case, it is with both dread and anticipation that I await the next installment.
IAmInHurt: I learned about the brain from reading a gorefic. Lol
Jaysontaylorblogs: As much as I love this.... I'm going to have nightmares for a few years now....
HELLKRINDER-NOI: I found this story on Deviantart after reading The Experiments of Twilight Sparkle,(which got me into grimdark stories). And I have to say, Im impressed and eagerly awaiting the next chapter(On a random note, don't kill Scootaloo)
Pony of Passchendaele: So...Only grim-dark, nothing even remotely perverted, like "The Experiments of Twilight Sparkle," and I think I know where this could be going, though I will not attempt to confirm as I hate spoilers. I have high hopes and congratulate you on your outstanding work. One of the best I have ever read, I have been desensitized for the last 3 days because of it...I am looking forward to the SATISFYING and COMPLETE ENDING to this wonderful tale.
LadyCobraa: I think it's safe to say that this is the best grim dark pony fic ever.