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Originally Posted by Rndm_Perfection
If the "real world" is really the real world, then how would it be destroyed five times and then be restored;
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Only Zion is destroyed, well the people are killed, the place is not destroyed. And there is some ventilation tunnels connecting zion to the upper world, they might be previous tunnels dug by the machines to kill the humans.
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how also could Neo handle the squiddy;
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That was one hell of a twist, and quite frankly I don't know how he did it. But I think that the purpose of that part was to put a doubt in our mind about the real world, but if it's really a matrix inside the matrix, it will suck. I believe that Neo is either a)now capable of some sick mind trick outside the matrix (

) or b) able to control the machines trough the matrix whithout being connected or c)something else that we'll learn in revolutions.
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why would the architect treat the one's purpose as part of the control, and tell him that if he were to enter the door to the mainframe, that his "code" (not sure the term he used) would be imprinted into the system. Similar to the last part, how would Neo imprint some code onto Smith if he didn't have a code of his own?
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I think that everybody inside the matrix has their own code, human or not. When your mind is loaded inside, it has to be digitalized, therefore, transformed into code. And the one is the sum of an inbalanced equation, that equation comes from the inconcious choice that every human being plugged into the matrix has (get out to zion or stay in), and that the machine (well the architect) can not resolve but can control by inserting the remainder of that equation into the one, and get that code back at the end to try to solve the equation perhaps? So neo has that code inside of him, giving him his powers, and some of that code got copied into smith when he destroyed him at the end of part 1. Remember the problem is choice (that's what the code neo carries is all about), and now Smith had the choice to continue being an agent or to become a rogue program, because of the code he carries. Anyways, that is what I believe.
That would be the reason why the matrix will crash if Neo doesn't salvage zion, because if zion doesn't exist, the people inside the matrix won't have that choice anymore, and like in the first versions it won't work.
I don't know if it makes sense, but that's my take on it.
Man, what I would give to sit with the Warkoskys (sp) and get all the proper answers.