As for why the agents are trying to kill Neo...they don't know any better! All right, so now we have three or four theories to explain away this inconsistency. So they're testing him. No, they're forcing the prophecy to come true. Or are they simply low level programs just doing their job? Or maybe they don't know any better! Yeah, it all makes perfect sense now. ? Are you guys still going to claim this isn't a plot hole or at the very least a plot inconsistency? "Surely you can do better!"