Adachi, Dojima's assistant, turns out to have been the murderer of Mayumi and Saki.
Namatame was the one who kidnapped the high-schoolers and put them into the TV world, but he had no intention of hurting them.
Mitsuo Kubo (that creeper kid who tries to ask out Yukiko) killed Mr. Morooka because he wanted people to think that he did it.
The parking attendant from the beginning of the game, who shakes your hand, is actually Izanami, who gave Izanagi (the starter Persona) to you. I don't know all the details about that part though, as I only got the ending where you battle Adachi and this other thing that looks like a giant eyeball.