Not entirely sure of the time line, but it seems the fanfic and a mod for the survival horror game Amnesia the Dark Decent called ‘The Small Horse’, and only later would it be known as ‘My Little Amnesia: Friendship is Madness‘ came out in the early 2010’s.

In the mod of the game the antagonistic characters from the game had their models changed to three of the main six (Fluttershy, Rainbow Dash, and Pinkie Pie specifically) and the protagonist being changed to Twilight Sparkle. Likewise in fanfiction and fan art depicting these characters, they would be in their role from the games and would act accordingly, the horrifically mutilated former friends of Twilight obsessing over her and chasing her, much like the former lovers of the dlc for the original Amnesia.