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The matrix within matrix is very logical, but I find that hard to believe for some reason. The hints are there, for instance as opposed to a greenish hue to the matrix, there is a bluish hue to the "real world". I may be over analyzing, but look when Neo wakes up for the first time in the first Matrix in the Nebuchadnezzar, the screen is all blue for a split second, almost like a system starting up. Furthermore the dream of Neo's of Trinity falling out of the building, Neo tries to tamper with, by not allowing Trinity to come into the Matrix. However a faulty bridge ends up killing the operator in the other ship and they can't avoid the machine attackers. As a result Naiobi and others sent in in Trinity's spot are killed. Almost as a way of showing that destiny can't be tampered with, because its all pre-programmed in one way or another. Furthermore, at that exact same time Morpheus is talking about how he doesn't believe in coincidence, or accident. This would suggest that the "real world" is under the control of machines-- a second matrix. The hints are certainly there in support of it, but it seems it would be alot to explain in a final movie.

I noted much the same on other forums about the bridge accident.

However it wasn't Nairobi that was killed. It was another black actress that resembled her. Nairobi was in the final scene on the hovercraft as it was her ship that salvaged Morpheus' crew..