I'm currently re-watching the three Matrix Films (The Matrix, The Matrix Reloaded and The Matrix Revolutions) and I have come up with a theory about it. No one is ever really outside of the Matrix, the Earth the Redpills know is another simulation, one designed to keep he humans under control and continuing to produce power.
Just watched Matrix 1 and Animtrix yesterday, and already found a lot of evidences in form of "chechov's gun" about not only real world is matrix second layer, but a Neo himself is a program, and it all ways right in a first movie already. Just a few examples of "chechov's guns" that giving out the clue that Neo is program and that real world is not real at all:
Neo is called a machine, many character wonder how neo acts similar to programs such as agents, but they excuse that by believe that he is "the one", without actually understanding the nature and purpose of "the one". Faith just makes them blind to hell lot of facts that gives out that Neo is a program, and that program cant exist in real world.
Indeed when you believe that world is real and that you already escaped Matrix you have no motivation to seek for further truth and try to free yourself from another layer of matrix.
Thats actually wha Architect was talking about - The Oracle found out that 99% accept Matrix if given a choice and yet only 1% still cant, for those 1% extra layer of Matrix was created, to give them illussion of choice, to make them believe they are free, whil in fact they are still in matrix.
The most clear evidence of this is ending of Reloaded and Evolutions, where Neo starts to have super powers in "real" world, he is confused to purposely confuse us to believe that such things could happen in reality, but in fact there is no logical way neo could stop machines by hand without any wireless signal transmiter in his body, which he lacks, there is no way Neo can see Bane as Smith with glasses in form of flames, this moment shows clearly that the one just realised that "there is no spoon" even in real world, so he can recreate it as well and see its "source" without eyes.
Whole Battle with Smith and the way it ended was a heavy reference to a description of how programs works in Matrix - once they done their purpose their process is terminated and they are returned to source, so once Neo realised that he and smith should end their purpose he stopped fighting and allowed Smith to pocess himself so that both of their programs could end with "return code" and allow matrix to reload. Whole Smith was not actually a smith it was a core of neo that refused to return to source because his purpose was not yet complete, under the shell of Smith. This is what Oracle tried to tell him.
There are more evidences, for example whole fact that mind somehow makes people bleed and die in reality - for real? At first i as many believed it was just underdeveloped fantastic element, but as more a re-watched this as more it was clear that this was done on purpose to give clue about virtuality of "real" world.
So called "real" world was created to be more realistic, with more strict rules, and when people had faith they already free they had no motivation to change "real" world like they did with spoon, so nobody except for Neo and Smith\Bane violated its scrict rules and never notticed how absurd is the fact that taking injury in matrix somehow magically brings that injury in a "real" world. I believe this rule was set by architect to make life harder for those who refused matrix. Yet again, Neo violated this rule by getting into Limbo ave without direct or wirelss connection to Matrix.
This is imho is most heavy evidence of matrix in matrix and neo is program theory, since Limbo somehow connected "real" and virtual world and allowed as French-man says to bring things from one wold to another. How it even possible to bring something from reality to virtuallity and back? They only logical answer is that both worlds are virtual and Limbo just connected them, and Neo after confusion since partial realization that real world not so real, accidentally shifted himself to this intersection between worlds without any physical connection.
There are more things that hints virtuality of "real" world, like for example color coding of everything not real as blue and real as red - blue pill means you remain in virtual reality. Have you ever wondered why does real world is symbolically color coded in blue colors?
How come whole Zion could be built by few dozens of people?
And how come that one of the screens at Architects place some of video footage of Neo is taken from real world?
You've certaintly convinced me, every counter argument is very well thought out. I will have to watch the Architect and Oracle scenes again to get their meaning with this theory. I too have never been convinced by explanations for the "real world" superpowers of Neo and I did spot that screen in the Architect scene with Neo in the real world and thought it was odd. Not sure what you mean by the colour coding though.
I forgot to mention another good evidence that Neo is program - its the fact that he was dead in real world in the matrxi 1, but magically ruturned to life. Ok, i get it when it happens in matrix, he is uber cool, and can rewrite things, but at the moment he did his body was dead already, he cought out blood and his heartbeat stopped. How could he override that outcome in real world by overriding things in matrix? Only if real world is another matrix and neo is program.