The Matrix

[LiquidDamage]

The last scene of the movie adds substance to my theory.  At first I thought the other ship emp'd the sentinels that were about to attack the four remaining humans but perhaps Neo figured out that Zion-world is just another level of the Matrix and he chose to bend the rules here too.

I see no reason to say that the "real world" must be another Matrix, as I can think of other (more interesting) explanations for Neo's actions at the end, and Smith's little trick.

The first thing I thought when Neo stopped the sentinels was, "He can affect the machines outside of the Matrix, because his mind is actually a sort of missing link for their programming". Neo didn't freeze them in mid air like he does with bullets, they emitted electricity like how most sci-fi movies show robots short circuiting. All we saw was his power over the sentinels, there was no demonstration of power over anything beyond those machines in the "real world".

This doesn't rule out the idea of the "real world" being a Matrix of its own, but until I see Neo fly, punch through solid concrete, or dodge/stop bullets outside of the Matrix, I'm going with "he has power over the machines".

I feel I should mention that Neo is the only version of "The One" to have lived past the choice the Architect confronted him with. They may do something with that-- perhaps he will continue to learn new abilities that the others were not around long enough to explore. This control over the machines may actually be the result of his decision not to return to the source, as he now has a greater understanding of how he relates to the machines.