I saw the Matrix and thought it rocked. Im a huge matrix fan a an even bigger computer geek so when I watched the movie tons of things made sense to me so heres my take: [sp] In the Matrix he can change rules...he is part of a program or at least a interactive piece of a huge program. When he stopped those Sentinals when he left the "Matrix" he said he could feel them...... SO check this out... A program is bunch of small scripts or services working together or against each other...queries, rules engines, logic, etc. It is logical to think that Neo would be able to "feel" the Agents arrive at that meeting in the beginning of the movie like he did.
However that was a different feeling or at least a different reaction and emotion on his face for that then when they left the "matrix" and were chased by the Sentinals. He was actally surprised he could feel them and said something is different. SOOOO IMO.....I think that they are not in another Matrix but actually part of a network now. They are each nodes.. Like on a network, each node sends out Pings or broadcasts letting each other know where they are and who they are. Programs don\'t let nodes know this stuff, programs just let other parts of the program know whats what.
So, Matrix .... huge program.
Out of the Matrix, still virtual but each person is actually a node with a Address that broadcasts[/sp]