I have some ideas regarding the Matrix-Reloaded theories. Why do the machines allow the humans that reject the matrix programming to survive? In the first movie when Neo “wakes up” a worker robot come by and unplugs him. He then is ejected out and down a tube and picked up by Morpheous and crew. But why is he allowed to live? Why don’t the machines just kill off anyone who wakes up? Maybe they didn’t really get unplugged? I think there is something to the multi-layered matrix theory. When someone rejects the programming and wakes up from the primary matrix, they are then routed to the sub matrix programming that they think is the “real world”. They are in fact still in the matrix, plugged in and supplying power to the machines. The whole idea of Zion and the war are to supply the humans another reality to accept since they rejected life in the primary matrix. However, Neo has once again awakened from the sub matrix when he realizes this truth and is able to “feel” the machines near by. He then is able to stop them with some kind of EMP blast even though he is in the supposed real world. He really is in the sub matrix world and now realizes that he can control the environment there too. This also explains why the Agent Smith program has figured out how to leave the primary matrix and has taken possession of a body in the sub matrix. Lets see if I fully understand the choices he is given in the end. The door on the left is going back in to the matrix where he is able to save Trinity but at the cost of letting the machines find and destroy Zion. Because if the machines let too many people wake up from the primary matrix then this will cause to much instability in the system. They will start to loose too many people out of the primary matrix at too fast a rate (Morpheous says during his rally speech that they have awakened more people in the last six months than they had in years.) Currently they estimate only .001% reject the initial matrix programming. Once they have a certain threshold of people in the sub matrix then they sort of reboot or flush the system and let them start all over. It’s happened 5 times already. The door on the right leads to the primary matrix core and Neo could possibly destroy the matrix all together but at the same time killing everyone who is still connected to the matrix (which is everyone). He really cannot take that choice because he would be killing the entire human species to include himself. There would be nothing left except the machines and whatever existence they are prepared to accept like The Architect says. Can anyone correct me here if I’m wrong or add anything?