Ever hear the phrase <better the devil you know>? Naoi, the vice-president of the student council is now acting president, and he's even tougher than Tachibana. Plus he's an NPC, so they really shouldn't go after him.
Otonashi reaches out to Tachibana, but Naoi imprisons them.
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.