Im agreeing with Chekhov to a large extent and Im guessing the BO is actually developing something AI. Itakura mentioned something about humanity. Perhaps his program was actually still not dangerous but BO wanted him to add in some small feature which rendered it dangerous. We have to understand that, Aoyama's "humanity" was defined at the time when it was aired. It could be a controversy at that time when it is not now. AI is also something which was debated about a while ago. Could it be that, the BO wanted him to produce some program which is able to function like a brain? We know of stuff like Neural Networks now. Could it be that Itakura was building something like that for his chess game so that the system is a highly advanced system which can learn moves to counter the opponent, but now he was forced to complete it for an actual human?
Since "revival" was mentioned, could it be that BO wanted to plant memories into this "artificial brain" and place it into a person and use the APTX4869 to keep that person alive forever??? o.O