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OK. This post is a mix of speculation, symbolism, and spoilers. The GUT of Reloaded is this: The Matrix was created to control mankind. The first Matrix was a utopia-like world, but all the "copper tops" rejected the Matrix and entire crops were lost. So The Architect built the current Matrix to simulate our world at the end of the 20th century. Their simulation couldn?t' be perfect, and so there were anomalies. That anomaly manifests itself in Morpheus, Trinity, Neo, etc....anyone that has been unplugged because they can sense the Matrix is all an illusion. A small percent of those (1% of the 1%) people have the ability to control the Matrix itself, ala Neo and the One. The problem of The One and the anomaly (Trinity and gang) has been solved by creating the Oracle/Keymaker/Architect (they are in the position to guide The One down a specific path). This path leads to the destruction of Xion (and all the people that have been unplugged) and the rebooting of the Matrix. This resets the equation, ensuring not too many people ever escape the Matrix to be a real threat to the machines.
The Matrix has been "Reloaded" 6 times. The head of the council is in fact the previous One before Neo. All the other members of the council are also the original progenitors of this current version of Xion. That's why they insist that Neo must be in the Matrix (they know the cycle will repeat and he is the critical carrier of the code). This time is different however. Neo is different than all the other One's before him. The difference is Smith. Note that in Neo's Convo with The Architect the TV's showing Neo's possible (and probable) reactions all show very emotional responses...something the machines themselves define as typical. Neo is somehow different...he is more like a machine showing little emotion (not just Reeves' bad acting either). The Architect also notices this but doesn't quite get it. He frequently comments that Neo is "different" and that he figures things out "faster" then the previous incarnations of the One. That's because his "code" has been tainted/bettered with a portion of Agt. Smith's code.
The other reason this time is different is because of Smith himself. When he exchanged code with Neo (when Neo seemingly destroyed him) he was essentially freed from control. He is now a free roving sentient program...much more human then his counterparts. This has been already examined by other posts (his multiplication, which is akin to a virus both computer and biological). In the first Matrix Smith likens humans to a virus saying that they multiply and consume RESOURCES until all RESOURCES are gone. This is vital to the trilogy. Smith and Neo will ultimately destroy the Matrix together. Smith will infect everyone in the Matrix (like a virus eating up the RESOURCES of your computer/network) and Neo will be forced to defeat him, thus destroying everyone in the Matrix. Neo and Smith are foils and are both equally important to the end of the story.
Some of the things Agt. Smith's code has enabled Neo to do are very different from the capabilities of all the other One's...his different reaction to the Architect, the different door, flying faster then has ever been seen in the Matrix (when racing to save Trinity). His ability to save/resurrect Trinity is also a big indication he is something the Machines didn't count on (can you say Lazarus anyone?). What Smith's code has done has been to free Neo's mind even further. **Speculation** Either Neo is now so "free" that he is utilizing other parts of brain never before used (telekinesis, telepathy, etc) or he now is part machine so much that he can control the machines outside the matrix (they are all networked together, so why not?). It could easily be both. I doubt very much that the Wach. Bro's are stupid enough to make a Matrix w/in a Matrix.
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