Real Life Writes the Plot: The entire fic got started because of a YouTube comment. The entirety of the comment, however, has not yet been revealed, as it contains an implication that could be considered a spoiler, but it's clear that the whole thing got started with the idea of Twilight turning her friends into books.
Additionally, the opposing, Split Personality-like aspect of Twilight and her conscience was inspired by a scene in the MLP episode Lesson Zero.
Even further, and easily the most disturbing, a majority of the torture methods (especially done to Fluttershy) actually exist in Real Life (see above Wayback link).
As is revealed later, Twilight's plan to eradicate disharmony by murdering all disharmonious life is based off of the Nazi's and the Holocaust.
What Could Have Been: The entire fanfic was originally going to be a short one-shot, basically going with the whole thing of "Twilight turning her friends into books". Of course, it obviously expanded far, far beyond that.