My friends and I have come up with a Matrix within a Matrix theory. Where the "real world" is actually another Matrix. This would be (in some peoples opinions) a more simplistic way of explaining Neo's powers at the end of the movie.
However, a more theological approach to the situation, would be that Neo was granted such powers in the real world so as to battle his greatest adversary Agent Smith.
I think what some of you aren't realizing (and I haven't come to fully comprehend because I don't remember every aspect of the film), is that when agent smith copied himself into that man's body (when they were trying to escape with the message from the Oracle), and then was taken out of the Matrix, Agent Smith's ego, or at least a copy of it, was also taken out of the Matrix. It manifested itself in the human body of the person it copied itself into.
What I don't understand is the guy hooked up to the machine next to Neo at the end of the movie.
Did anybody else notice what he etched into his hand when he tried to kill Neo? A Roman Numeral two. Which could be indicative that there is not only a "One", but a "Two". I think it was confirmed in an interview with the brothers that there would be a "two". However that design he etched in his hand could have been something else that I didn't think of. Just a suggestion.
Oh well. I think I've milked about all I can out of the movie for only have gone to it twice. I'l have to go see it again.
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