The Mysterious Boy, aka the AI, was created by the Programmer as the first NPC in the Afterlife. The Programmer's details match that of Otonashi's with striking similarities. Let's not forget that alongside the original ending of Angel Beats, Key issued another epilogue, aptly titled "Another Epilogue". In this, the main focus is another person that's arrived in the Afterlife, and he is surrounded by quiet, obedient NPCs. After challenging the reality of the Afterlife School, he is talked to by the Student Council President,
the Otonashi in an alternate timeline, who hasn't moved on yet,
and he is told that if he has any question about the world that they both live in that he should come down to the Student Council room. However, as
Otonashi heads back to the Student Council room, a girl can be heard saying, "There's a rumor that he's waiting for someone."
So therefore, it's entirely possible that
Otonashi is waiting for Kanade, and that this timestream somehow loops. Otonashi goes crazy waiting for Kanade, who has an infinitesimally small chance of reappearing in the Afterlife, but still, better than zero.
He turns himself into an NPC to be able to withstand the long wait, and creates the AI, or the "Mysterious Boy" to be able to maintain the requirements of the Afterlife, not allowing love to manifest, therefore possibly saving future arrivals from the pain that he has been exposed to. This may be why he creates Angel Player, because he knows that if Kanade reappears, then she'll know how to use it, and maybe program it to move him back from his NPC state. The members of the SSS arrive after this. Then, at the time of Episode 1, the timestream loops, causing
Otonashi to revert back from an NPC.
Forgetting everything that's happened to him, the events continue their course the same way they did before,
causing the timeline to repeat over and over and over.
Any thoughts? This seems pretty far-fetched, but it's out there now.