So, you are saying this should have been just a psychological story exploring how the rest of the class suddenly disappearing, without a trace, would affect the lone "survivor"? No supernatural stuff aside from the others being gone in a flash of light. He would have gone through a bunch of interviews by the police and psychologists, and probably got harassed by journalists, but that's pretty much it. Maybe, since it's Japan, he would have later been bullied. Otherwise he would have been just like any other school kid, continuing his daily life, maybe being affected by survivor guilt if the author so wanted, but likely not since he was a fresh transfer student.
I can't say I'd have read such a manga.