Nonomiya's encounter with the Principal in the alley. Whenever he turns away from the Principal, he's always there in every alleyway that Nonomiya is at. And he knows his name and class. And he intends to eat him.
The Principal suddenly appearing and devouring Yoko's soul.
The Principal in general really. From bizarre appearance to facial gestures to overall personality, the Principal is oddly one of the scariest things this troper has ever seen.
The ending to Chapter 5. Maybe a little exaggerated but still, this troper will never see rabbits quite the same way.
Midori's face after when she remade the contract with the Black Tea Gentleman and goes back into her fake reality is particularly jarring.