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My theory is as follows, compiled from the game "Enter the Matrix" and the first two films. A tinge is from the preview for Revolutions on enterthematrix.com. Things to remember to understand my theory. Neobi talking to the Oracle. "Neo has touched the source, he is between worlds, Trinity will have to fight like hell to get him back" (summarized). Remember will all computer systems everything is connected. The sentinels are connected to each other, to the matrix and so on. Neo touched the source of the matrix, this touched a long outreached arm to everything connected to it, sentinels included. When he left the Architect, he did return to the matrix, and then to Zion. I believe Zion to be in the real world. Like stated in one of your comments that the machines keep wiping out Zion and then rebuilding to try and understand humans and figure out why they can not fully control them and keep a stable version of the matrix. The kicker is this time when neo is unplugged a piece of him is left behind. A connection. He dose not realize this. But notices things like sensing the sentinels. This would support the wireless theory. Just like the end of the first film, Neo realizes he is the one and how to tap into the matrix, from within it. A direct connection. At the end of the second film he is beginning to realize he still remains connected remotely to the same system. He raises his hand and stops the sentinels. I believe the had raising is just for effect, like with the stopping of the bullets. But he was able to project the "commands" needed to shut down the sentinels because as I said before they too are connected to the matrix. The closer the got to him the better "reception" he received. But because he is in the physical world, his body is stressed to the max, and or he sends to much of himself through the connection placing the better part of his mind back into the matrix as if he were jacked back in. Since he is connected "even though remotely" his body does not die. The thing is he may not be able or sure how to get back, or is trapped within the matrix. Lord knows where in the matrix or of it's subroutines he is. But the preview shows and says a who lot of trinity fighting to get him back. (Her because of the who underlying love will conquer all theme). So I feel that the third movie will be a lot of everyone fighting in the real world of Zion, while trinity and subsequent others are trying to find neo to bring him back. Just as they are able too enter big ol neo agent smith fight scene. They get out, neo comes back, stops the machines attack. So now the machines being defeated in the real world, the matrix must go on for now. If you unplug everyone at once or two many there is no power. So the work begins to free the humanity from the matrix. All the while there are still rouge programs and residue from the machines within the matrix. So there will be fighting until the end. Enter the Matrix Online... that’s just my opinion. Did any of what I just said make sense?
Prolly needs to be expanded a bit more to cover my holes, but I’ll save you that…
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