Somewhat experienced poster
Posts: 16
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In a nutshell..
The Matrix is the Matrix, being what M1 called a virtualisation of 1999.
Zion is also a virtual world, alongside the Matrix. As per the Architect, it is a way of controlling those who chose to leave the Matrix. It is the solution which the Oracle 'stumbled upon'. Inhabitants of Zion are still plugged into the power grid without their realising it - they think they are out. Zion is the virtualisation of the world that humans expect to see when they escape from the matrix.
The One is a tool of the Machines as part of the Zion "contradictory systemic anomaly" control mechanism. Neo is the 6th in the cycle, each one is 'improved' over the one before as part of an iterative system tuning process.
The updates to the Neo version of The One introduced new or strengthened capabilities within the virtual worlds of the Matrix and Zion - love, flight etc. The Oracle introduced those changes, she wants an end to the war.
The Oracle did not know beforehand what the full impact would be of the changes introduced to the 6th One. She tells Neo that he suprised her, and it is those changes that created the Smith virus.
The Smith virus is eradicated by Neo and the Source working together as the Oracle predicted - Neo gets inside Smith and the Source does the rest.
Once it's all over the Architect chastises the Oracle for playing a 'dangerous game', her reply of 'change always is' reflects the Oracle's desire to end the war - which she has done. The Oracle is responding to a growing recognition within the machine world of the concept of 'love', as shown by Sati's parents and by the experiences of the Runner machine in Matriculated (Animatrix).
The Architect is not happy, but agrees to release the "ones who want out". These are the people currently in Zion, they are the only humans plugged into the power grid that have chosen to get out at this point in time.
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There we are.
I think that answers to the frustrating questions can be reasonably found within this theory, for example Neo stopped the machines in Zion with his hand because he is programmed to have special powers in both the matrix and Zion virtual worlds - he just "didn't know it yet" - and the Oracle's explanation does make sense with this theory.
Feel free to try and shoot it down, it will be a good test. At least for the moment I feel satisfied that I know what is going on, and can lessen my disappointment in Revolutions.
I've left out a lot of supporting detail, don't want to bore people. And for those who seek deeper meanings through allusions to religion etc., yes I think they are there but the underlying story does not require them.
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