The mysterious boy appears in episode 12, who created it?
1 - a curiosity, it is not said if the Mysterious Boy is an NPC or a person, but he says he is programmed to watch the computers and see how much love is in the Afterlife. When love began to manifest in Afterlife, he probably activated the Shadow Program to kill everyone, so he is an NPC? as far as I know it is impossible to program a person.
2 - Angel Beats is a game? the reason why I started to have doubts that is, in the anime and manga all they talk programming, NPCs and Etc ...
Otherwise the Mysterious Boy says he was programmed to activate the program of shadow creatures.