Hmm this is interesting. If this is a "game world" per se and the MC is a player, then that each time the assimilation rate falls, the closer he gets to his original reality. Perhaps he was a person in a VR game that assimilates you into the game to the point where you don't realize you are playing it and as your assimilation rate falls the more you remember of you reality. Of course the fact that the game characters are aware of non-game characters, or guests, means that it's not just standard VR, but full blown AI? And not only that, but an AI program that has the ability to interfere with the "real world"?
That would explain the save load feature that skelly has been going through.