1) Quirrell believes that bringing back Hermione would be the surest way to prevent Harry from destroying the world. (“Miss Granger was the only one whose worries he truly heeded—with her gone—all checks on the boy’s recklessness are removed”; “You truly do care about that girl (...) I do not understand it, but I know the lengths you will go to because of it. You will challenge death itself, for her. Nothing will sway you from that.”)
2) Preventing the prophecy from coming true appears to be at least one of Quirrell’s top priorities as of the Roles arc (which, for some as-yet unestablished reason, the beginning of the unicorn deaths falls into).
3) Quirrell has been killing unicorns and storing away their flesh.
4) Eliezer has said, as above, “I’ll state outright that at the end of the story Hermione comes back as an alicorn princess”.
Semi-serious hypothesis: Quirrell is intending to bring Hermione back using unicorn blood.
Then a final gesture from Professor Quirrell ripped a huge chunk out of the unicorn’s side, leaving behind ragged edges; the raw meat hovered in the air, then wavered in Vanishment and was gone.
OOC as a joke in one of the author’s notes.
Though, mind, he could be telling the truth.
Given that:
1) Quirrell believes that bringing back Hermione would be the surest way to prevent Harry from destroying the world. (“Miss Granger was the only one whose worries he truly heeded—with her gone—all checks on the boy’s recklessness are removed”; “You truly do care about that girl (...) I do not understand it, but I know the lengths you will go to because of it. You will challenge death itself, for her. Nothing will sway you from that.”)
2) Preventing the prophecy from coming true appears to be at least one of Quirrell’s top priorities as of the Roles arc (which, for some as-yet unestablished reason, the beginning of the unicorn deaths falls into).
3) Quirrell has been killing unicorns and storing away their flesh.
4) Eliezer has said, as above, “I’ll state outright that at the end of the story Hermione comes back as an alicorn princess”.
Semi-serious hypothesis: Quirrell is intending to bring Hermione back using unicorn blood.
http://hpmor.com/chapter/100
Though unreliable narration is always possible.