Either the author really has the balls to kill off almost the entire cast, or there's something going to happen later on that somehow brings them back. Personally I'm expecting the last possibility. It doesn't really make sense to kill off EVERYONE after we finally start to get to know the main characters. And remember! Kishimoto's original self is still alive, so she might be brought back into the story somehow, even if that version of her isn't a part of the game.
But who knows, this story is crazy enough to simply keep them gone for good and continue with Kei and any new participants in later missions.