Yume Wo. (夢を。)/theories

Father's sin
From events and ending seems to that in Family Massacre guilt is Nagatsuki's father, probably he planed that Nagatsuki killed his mother and himself, for this he made a special tea that Nagatsuki-kun drank, but in fact his plan was backfired at his father and Nagatsuki killed both parents, not in his mind.

Friend among the enemies.
It can be that calm smiling chaser Yujin, who gives Nagatsuki a school uniform was his friend, and when they were friends, bullies didn't bully Naga-kun, but fake, obviously Nagatsuki been in Yujin's debt.