As always, I think the monkey is on (to) something.
I just got back from seeing it, and the wife and I were thinking quite along the same lines as Lewk (scary thought, isn't it
)
There are many things that point to the "outside" and Zion being simply another layer of the matrix. I think one of the key moments is the conversation with the architect, where he tells Neo what I think is the truth (for the most part) but isn't telling him the whole truth. He says the Oracle is the mother of the matrix, and had discovered a way to give choice to the people. So, 99% of people live happily in the "matrix" and 1% "choose the blue pill". Well, they aren't just going to toss away that 1%, so they have an "outside" to the matrix, where the "blue pill" people think they have escaped thier prison walls to when they have merely escaped into a different part of the prison.
Another key point, is that Agent Smith can still control the guy once he is "out" of the matrix; the fact that he no longer looks like Smith once he's out, is simply a device to keep the audience guessing. He is no doubt the one that set off the EMP, and is the one laying on the table next to Neo at the end.
I think the first hint at a matrix within a matrix was in the first movie (and again in the second) when Neo and Trinity exert control over life and death in both "worlds" simultaneously. Though, it only makes sense in retrospect, because its easy enough to come up with other interpretations.
For me, what sealed the deal on my opinion of how it works, is when Neo said "he felt" the sentinels at the end, even before he stopped them. I had ventured a guess that the two worlds were in fact nested matrices, and had realized that now w/ Smith on the "outside" that some code would have leeched over the boundary, and what would stop more from going over, so I was sort of looking for something like this. Neo's abilities seem to be coming with him back to the "real world" now, though, not without difficulty.
Agent Smith, hmm; I love this character, and the actor that plays him .(Hugh Leaving I think, he also plays Elrond in LOTR) I tihnk that at the end of the first movie, when Neo "kills" him, Smith, as a sentient program, starts to understand how to exert control over the matrix like Neo does. He combines that with the abilities his original programming as an agent gave him, and viola, that explains what he can do, but not why he does it. As my favorite monkey pointed out above, Smith very clearly describes his hatred for humans and the matrix, hence his desire to kill off the humans, and consequently Neo, because Neo is supposedly the savior of humankind. What Smith doesn't know (yet) is big picture, about the rebuilding of the matrix 6 times before, and that the matrix has intentionally set Neo up to destroy the matrix (actually, just the inner layer of the matrix) so they can start it over again. If Smith understood the big picture, he wouldn't be trying so hard to stop Neo; he's more of a rogue program now. I think that for the third one, the big picture will be explained to Smith, and he will kick into overdrive to stop Neo and company from destroying the source to put a stop to all layers of the matrix.
Ok, enough of my rambling, back to your regularly scheduled programming
