// THE FOLLOWING CONTAINS SPOILERS OF THE MOVIE PEOPLE NEED TO SEE
What you are about to read is highly classified in the eyes of LAW (Larry & Andy Wachowski).
I’ve finally figured out their little scheme. Never mind that I had to wake up at four in the morning to stand in line for the six AM showing of The Matrix Revolutions IMAX Experience just to understand, it was well worth it. Of course once I was in the theatre, I still had to wait half-an-hour for the movie to start. Actually the only preview we saw had trailers in it. Huh-huh. A trailer of trailers. It was for the NASCAR Imax Experience. Coming Soon to an IMAX near you. But beyond that the theatre was packed. Because there wasn’t a midnight showing. The film was being globally released at the same minute all around the world. Which is pretty damned cool if you ask me (although I didn’t feel a tingling sensation of kinetic energy as half the world’s population did exactly what I was doing…oh, that’s because we were sitting…it only works if everybody runs). So you go through the movie (a little confused if you haven’t immersed yourself in the interactivity of LAW’s universe (Enter The Matrix, The Animatrix, the comic books, etc.)) with enjoyment as you watch the rebels defend Zion. But then the movie ends. And you get confused. Want help?
Spoiler Alert! (place and hold your mouse over the bar to see)
There is no Matrix inside of a Matrix. There is the real world and the Matrix. The architect created the path of the one when he redesigned the matrix the third time (1st time = utopia, 2nd time = no choice, 3rd time = choice) to balance the equation. The One’s purpose is to "reload" the matrix every one hundred years (Morpheus says they have been fighting for a century, so give or take, that’s the length of the cycle) when the machines destroy the rebels (real people) and the One’s code is re-inserted into the Source (machine mainframe) to restart the cycle and chooses 23 people from the Matrix to restart Zion. Or he can choose the door on his left and go back to the Matrix (for whatever reason), but 24 hours after that, the Matrix will crash (because it doesn’t have the "One’s" code which would have "reloaded" the Matrix) killing all the occupants. When Neo was plugged into the Matrix by the Source (the face in 01, the machine city (didn’t anybody watch The Animatrix!)) he became a conduit for the Source to eradicate the Smith virus, which happened when Neo surrendered to Smith and the Smith’s exploded in a blaze of white light. Then Neo was killed so that his "One" code could be reinserted into the matrix and "reload" the matrix.
. . . except for the sentinels and the bombs Neo stopped while he was blind.
My best guess is that Persephone’s kiss in “Reloaded” enhanced his brain somehow so that he could recognize programs outside of the Matrix. It’s kind of like a program radar, which is why he sees gold code. Remember how Seraph looked in “Reloaded”? He was a gold-coded program.