okay.. i just saw wthe movie last night.. Here are my (and Peutetre's) thoughts
We agree on the whole "second matrix" thing..
actually we think of it as a multidimentional array.
The matrix is an array within an array.
Also we think Neo may be a program. Specificly.. we think he may be a manifestation of error handling, or an "garbage collector".
When the oracle is talking about "ghosts, aliens, werewolves and vampires.." being programs doing stuff they arent supposed to be doing and they get a choice to shut down and exile themselves or get destroyed/ assimilated into the sources.. we think that may specificly alluding to Neo's role in the whole thing. Perhaps Zion is that exile? Perhaps Neo being the anomaly and all his powers stem from him being a conglomoration of errors in the programming. The Matrix keeps running him through the program trying to correct these errors over and over again until it's rate of failure is minimal. That is what the architect says that they have done this 5(or 6?) times previously. Theoreticly he's stuck in a "Do Until" loop.
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