Science Fiction Heresy, Part II: The Matrix
First of all, it seems to me that there is a parallel between the Matrix trilogy and the Dune Chronicles. In this analogy, Neo is the obvious counterpart to Paul Atreides with several points of similarity:
- They are both associated with messianic roles (The One vs The Kwisatz Haderach) that they are fated to discover as they contend against their opponents.
- Both Paul Atreides and Neo pass through an extended period of near death before their final climatic battle. For Paul Atreides, this was when he drinks the Fremen water of life and lapses into a coma which the Fremen interpret as a gathering of power within a spriritual realm. For Neo, this is the interval in which he has somehow transferred his mind into the Trainstation, leaving his body inert.
- Paul Atreides is blinded near his (presumed) death at the end of Dune Messiah, but still has his oracular vision. Neo is blinded in Matrix Revolutions before he sets out for the Machine City, but he can still see the gold code.
- Zion, which becomes Neo's place of refuge after the events of The Matrix, seems to be a parallel of Sietch Tabr, the Fremen desert base that harbors Paul Atreides after the reconquest of Dune by the Harkonnens. This seems to explain the rave in the Matrix Reloaded, which comes across as a watered-down version of the Fremen sietch orgy.
Extending the Dune analogy a bit farther gives an answer to one of the hotly-debated mysteries of the Matrix Reloaded, Neo's real-world ability to disable the Sentinal machines. The Dune parallel suggests that Neo posseses this ability in the same way the Paul Atreides possesses his oracular vision: each is the product of a long-term breeding program instituted for the express purpose of creating human offspring with certain advantageous traits. Neo is thus able to remotely disable sentinals, remotely transfer his mind into the Matrix, and other things because he was genetically engineered to be the next step in human evolution: a human who can mentally interact with machines without requiring the complicated architecture of the Matrix's life-support pods. In religious terms, the Matrix Trilogy seems to resemble something like a step towards The Omega Point in this interpretation.
My guess about the destruction and recreation of Zion with each iteration of the matrix is that it plays a role in advancing the goals of the machine's breeding program. In Dune, it is the Bene Gesserit school that is responsible for the breeding program that produces Paul Atreides. But another program of the Bene Gesserit is the covert manipulation of the religions practised on numerous planets throughout the galaxy. As the book reveals, the Bene Gesserit were planning to use control of the (necessarily male) Kwisatz Haderach as their means of gaining immense power and possibly control over the galactic empire. In order to prepare for this, the Bene Gesserit deliberately cultivated messianic imagery within the religions of the empire in order to manipulate the followers of these religions once a candidate for the messiah was ready.
In a similar way, Zion could be a convienient place to for the machines to deposit their candidate for "The One" and Zion's guerilla war against the Matrix could serve as the backdrop for testing "The One" to evaluate the extent to which the breeding program has succeeded or failed. The cultivation of messianic expectations for the Matrix within Zion's population would serve the purpose of protecting The One, and getting him jacked into the Matrix on a regular basis for closer observation, until his genetic potential could be fully evaluated. The necessity of destroying Zion with each iteration of the Matrix could be essentially cosmetic; leaving alive witnesses of failed messiah n is probably a really good way of destroying their confidence in the newly arrived messiah n+1.
For a final point, as of this writing I'm starting to doubt that the Architect was really being serious about all of humanity being extinguished if Neo made the incorrect choice. It seems very short-sighted of the machines to put "all of their eggs in a single basket", so to speak, and it also seems very self-serving of the machines to make sure that each Choosen One faces an inescapable, irresistable moral dilemma that practically forces each Choosen One to acquiesce to the machine's design. It would be pretty stupid of the machines not to keep some spare human genetic material lying around to repopulate humanity in case of emergencies. So I'm beginning to think that the Agent Smith virus was in some sense a bluff, and that all the machines really cared about was getting hold of Neo's DNA once they are certain that Neo had the genotype they've been trying to produce. Neo's resolution to reach the machine city, which would practically guarentee that the machines could grab his DNA once he died, seems to lead some credence to this view.
Once the machines were satisfied that Neo really was their desired end product and they obtained his DNA (since they carry off his body at the end), Zion would be purposeless for the machines and peace could break out. Similarly, there would be no more need to keep people trapped in the Matrix either; the next step in human evolution as planned by the machines was to free people from the physical Matrix all along.