Ok this is really aggrevating.here's my long ass interpertation of what the hell went on.
I'd like to start off by saying, I didn't catch the fact that Neo's mind stayed back with the source. But even if it did, and that's how he stopped the sentinals, how does that explain why the hacker infected by smith, bane, survive the sentinal slaughter?
There is only ONE MATRIX, because:
1) The Architect said that 99% of the people accepted the matrix's programming because while consciously they believed that they had choice, subconsciously they did not. This 1% of people have been and are eligible to leave the matrix by the so called "rebels" who were first freed by one of Neo's predecessors. The 23 people that the previous "ones" freed were the beginning of the New Zion. They went on to free more and more people until finally and singular anamolaic entity (the one) was found. The Architect said himself (go to another thread if you want to check out his speech with Neo) that this anamolaic entity while could not be stopped, could be predicted and therefore controlled, which lead "the one" to him. The reason Neo was lead to the Architect? Either,
a) Resistance starts building up within people and after a while the system must be "reloaded." This rebooting process can done by only "the one." If it is not done, people's resistance will build up so much that they will die, or cause the system to crash, killing them inadvertantly.
b) "The one" would be so much of a problem, and free so many minds, that the machines would die from lack of energy. While this contradicts the idea the Architect mentioned of them (the machines) being able to go on surviving without humans, it is much more efficient and easier to continue using humans as a power supply. In otherwords, it's easier for the machines to continue living off humans rather than finding the "other" way to surivive that the Architect mentioned.
2) One of the themes in the new movie is that everything has a purpose. The purpose of Zion is to facilitate the area where these one percenters go. Remember, if those one percenters stayed within The Matrix, they would wreak havoc on the system. The machines WANT them to become unplugged so that all will run smoothly.
If Zion is another matrix, or part of The Matrix, these one percenters would still foresee something "wrong" with the world and would wreak havoc on that system as well. Also, IF Zion is another matrix, why would the machines be encoded to exist on that level of the matrix?
Control?
I suppose so, but then why the massive cover up? Wouldn't it be easier to have an agent like program to keep humans undercontrol?
Another question can be posed as well, if Zion is another matrix. According myself and many other suscribers to this forum who agree with me, Zion is the place where these one percenters go so that that why won't cause a massive system failure of The Matrix. No one can argue that point. The Architect clearly pointed that out. Hypothetically speaking, if Zion is another matrix, or part of the one matrix that we all know exists, where do the one percenters of Zion go? There is always going to be someone who can see through things. That is the whole point of genetics. With any virus or epidemic disease that spreads throughout the world, there is ALWAYS going to be a handful of people who will naturally be able to resist it. It's been proven to be true as of now. There have been reported cases of people naturally fighting off HIV, an uncurable virus. These one percenters of the original Matrix are those select few who's genetic make up, or at least psyche is able to resist The Matrix. IF Zion is another matrix, then there will be once again a select few that will be able to see this.
I suppose one could argue that Neo is the one who would be able to see this. But then why didn't he see it right away when he was reborn as "the one?"
3) The Matrix within a Matrix theory is right because Smith was able to transfer himself into Bane, right?
Wrong.
In the first movie we learn that what ever happens to you in the Matrix, happens to you in the real world as well. After Neo fails the jump program, he asks Morpheus, "I thought it wasn't real?"
Morpheus: "Your mind makes it real."
Neo: "If you die in The Matrix, you die here?"
Morpheus: "The body cannot live without the mind."
So, when Smith sticks his hand in Bane and copies himself into Bane, he copies himself into Bane's code and takes control of Bane. In otherwords, Bane's mind is now controlled by Smith. What happens in The Matrix happens in the real world. So since Bane's mind was taken over by Smith in The Matrix, his mind was taken control over in the real world as well.
A more interesting question you all should be asking is: when they recieved the package, (a computer chip, i don't know what exactly it was) from the oracle to give to Neo, how did it transfer from The Matrix to the real world. Perhaps it was just information on a disk, and they were able to transfer it onto another disc, but it's still strange. Those who have played Enter The Matrix, see this again when Niobe and Ghost get the package left in the Matrix from Thaddeus, recording the Flight of the Osiris.
4) While Ush, and a few other believe the idea that Neo's mind and or code changed when he came close to the source, I did not infer that from the game at all. (Perhaps that is because i finished the game at 5am) While I don't not believe it, I am skeptical. Why was Bane rendered in the same condition as Neo, when it was Neo that brushed with the source?
What I'm implying is that when Neo jumped into Smith at the end of the first movie, something happend. Neo was copied onto Smith, and Smith onto Neo. Think about it. Neo knew that the agents were coming at the beginning of Reloaded. Neo wasn't surprised to see Smith after the Oracle left. Smith himself knew when an agent was going to arrive because during the Burly Brawl, one Smith copied himself into the agent.
AND in the teaser at the end of the movie, we see Smith being able to fly, and be just as powerful as Neo.
So, that is why Neo was able to "feel" the sentinals and stop them. It was something Smith could do, and combined with his own strength, he was able to stop them. Bane was able to do just the same, that is how he survived the slaughter they mention before, and he WAS rendered in the same state as Neo. However, the physical toll on him was too much, and that is why they become unconscious. Before, when in The Matrix, the toll was always on the mind, which Neo could handle just fine, but this time it wasn't.
For all those wacky theories out there that Neo is a machine, or a program, and that is why when he EMPed the sentinals, he hurt himself, is a bunch of baloney. If that were true, he would have died at the end of the first movie when they EMPed and killed all the sentinals that were breaking into the Neb.
There are my ideas, and I think without reasonable doubt that they are accurate. If anyone want's to dispute them, go for it, BUT you better be able to back up your arguements just as I have.