For those of you saying that Agent Smith loading himself into a real human and Neo being able to stop the sentinels is basically proof that it was a "Matrix in a Matrix." I'm of a different perspective now based on more input and thought.
Agent Smith loading himself into that character was basically an example of him infiltrating that person's matrix brain and then being transferred back to zion. In this case he overwrote the person's Matrix code, their mind basically, and then when it was uploaded back to Bane's brain, Smith was able to take over.
Although I do believe neo´s brain somehow has a link to the matrix here is the reason why. The sentinels communicate with one another and all the other machines/programs in the world via some form of super Wi-Fi I'm assuming. I believe Neo is able to tap into those transmissions now, because of his experiences with Smith and the Architect. He was enmeshed in their code and I believe took some parts of them with him. Smith commented on this point. I think that's why he was able to issue a "STOP" command to the sentinels by transmitting on that frequency, through the use of his implants, remember humans do have an electric current flowing through our bodies. As we are only using a very small portion of our brain power I doubt we know how to channel all of our capabilities. Neo has obviously reached a level, probably through his interaction with the matrix, that he is able to operate on a larger wavelength. He is already basically a cyborg. Man and machine, along with all the other people born into the matrix.
I know it's late but that's my .02
Can't wait for Revolutions....
