Ok. None of you know me, and this way to late for anything of a sort, but I feel i should say my piece anyway. Morpheus is describing Neo from the prophecym which, if you were paying attention to Reloaded, you would have heard that the prophecy was bs. And in the first one, the guy that was born in the Matrix who could control it who gave them the prophecy, he was one of the last 5 "Ones". The Prophecy was bullshit fed to Zion as a way to give them hope. As for powers going into the real world. The source is universal, for all programs, all AIs, all machines, and all of the like. Therefor, when he connected with the source, he stayed connected, or at least a part of him did. So in the real world, he can see them, and he take there metallic asses down two. And seriously, dumbf- dumbshit: what plotholes? Maybe if you payed attention to the DAMN MOVIE, you would have noticed that everything was covered.