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My theory which I've co-opted from someone else is that neo, trinity, morpheus are all programs desgined by the machines that are produced to continue the cycle of the matrix reloading and that it is smith who is the one we should be looking for. I believe that zion is a metamatrix and that above ground the humans are still fighting the machines, but have infiltrated the matrix by sending a rogue program (Smith) to kill Neo to stop him from being able to make that final choice, thus bringing the end of the matrix. To what end? I guess we'll have to see in Revolutions. It's a far fetched idea that Smith was sent by the 'real' humans to destroy the matrix, but I like it and am sticking with it. In essence, Smith really is the one, the one who represents humanity's survival against the machines. Any thoughts, feel free to bash or support.
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