Naoi is not an NPC. He's been balancing his goody-two-shoes student council behavior with vicious bullying, which is why he hasn't vanished.
He's decided that he's God. He's trained himself in hypnotism and tries to eliminate his opponents by giving them false closure.
Otonashi and Tachibana escape their prison to save the others at the last possible second.
Otonashi reaches out to Naoi, and we learn about his life.
Will this defang him?