The idea of a murderous Fluttershy is by no means new, with Pattycakes and Pony MOV popularizing the concept long before these two stories were created but they dwelved into very dark subject matter as it had Fluttershy manipulate Scootaloo into killing her victims while convincing the filly it was a "game".
In the prequel to the Day of the Filly story the reader is taken into a dark journey through Fluttershy's troubled mind as she experiences a severe mental breakdown - becoming more and more angry with everyone and everything around herself, mixed with hatred.
Her psychosis grew steadily worse and worse as she struggled to control herself, coming across the Cutie Mark Crusaders she once again became consumed with hatred and tried to hide from them.
Yet fate would have it the troubled Fluttershy would be found by Scootaloo, who continually tried to comfort her and unknowningly put herself in extreme danger as the unstable Fluttershy began to lose what little control she had and convinced Scootaloo to follow her home.
When Scootaloo went to Fluttershy's home things degenerated as she instructed Scootaloo to sit in the garden as she went into the house and went into a chest filled with clothes and accessories, which she proceeded to put on at random, becoming a "colorful clown of a pony".
When she did this Fluttershy found herself smiling, breaking down as she looked to a terrified Angel and began to state how things were going to get better, beginning to form a plan for a special game.
Fluttershy then goes back to the garden and asks Scootaloo if she'd like to play a game and when Scootaloo asks what the game was going to be Flutetrshy replied that it was a surprise.
Day of the Filly
Following the events of "Monster" Fluttershy takes second place to Scootaloo, who is manipulated into killing Big Mac, Applejack and Rainbow Dash - in the end Twilight manages to stop Scootaloo but is hit from behind by Fluttershy, dressed in her clown outfit and Scootaloo finally states she doesn't want to play anymore.
At this point Fluttershy notes that it was never a game, that Scootaloo had played her part and as Apple Bloom and a large group of ponies arrive (presumably to try and stop the pair) Fluttershy ends by saying "they will be so thrilled when they've seen what we have done, you'll see.. you'll simply.. die".