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Location: uk kent
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I believe that yes zion was amatrix within a matrix, but also zion was also meant to be taken as the real world, what do I mean? well the matrix within a matrix plot line if made blatent would have confused a hell of a lot of cinema goer's and perhaps only the most commited techno dude would have understood it, the films were designed as a good popcorn muncher for the average joe, but also had enough clues for a deeper plot line for the more avid fans. genius really, because it keeps you thinking, and makes the films repeat veiwing afairs, instead of one time action flick. so heres my interpretation.
The machines captured humanity and used them as batteries, and the matrix was created for mental stimulae, however this subterfuge was realised on a subcoscious level by a percentage of humans, and longing true freedom, the minds of those humans broke free of the designated area in which the machines could manipulate and control thoughts, and created zion, like a dream within a nightmare created by the minds of humans, the reason the humans can do such amazing things within the matrix is because they dont believe in the rules set by the matrix, and are only restrained by their minds imagination, in the zion human construct however, this bastion of mental freedom and sanity, robs the humans of their ability to think outside the box, for zion to be a refuge, the mind must believe it is real.
The machines software regularly wipes out zion, but it is always created again, the machines alllow this, because they recognise the impossibility of fooling all of the minds in the matrix, and understand a human made refuge will always reapear, however it must never be allowed to become too strong, or it would begin to disrupt the other humans in the matrix proper, so yes this is why the architect told neo that zion had been destroyed before, and remade repeatedly, if zion had been real and destroyed before how did the weak and antrophied humans crawl out of the tubes, feed themselfs, and then rebuild the machinary to create air and food etc, unless it was created from the imagination of the "free" human minds.
The one is a unique human, even rarer than the others genetically, who can see out of the box even more than the others, and can actually subconsciously see the real code of the matrix, even in zion, hence why neo could blow up machines with his mind in the "real" world. (how else would he be able to do that?) another proof that the "real" world is not real, is that agent smith managed to hack into a person in the "real" world, however on this occasion the one was far more gifted than before, and the software designed to subdue him needed upgrading, agent smith when destroyed by neo in the first film, was recreated by the machines and improved using infomation gathered about neo when he made contact on a code level with agent smith, so that smith had no restraints, as neo had no restraints the program to control him needed to have no restraints to be successful,(made to balance neo in the equation) however this meant that agent smith was beyond control, and he began to take over more and more space up for himself, threatening the entire matrix, and possibly crashing the whole thing. when neo at the end of reloaded destroyed the machines in the "real" world by instinct, (and a deeper understanding, that zion might not be real) he found himself at the outside the "entire" matrix, the train station,(the loading point for programs into the matrix) he meets a couple of programs trying to send their daughter into the matrix, knowing that with the chaos within the matrix caused by humans, their program will be hidden from deletion, as oposed to outside the matrix, within the core operating system of the machines, (programs without a purpose are deleted) neo has no power here, as this is outside the matrix completly, hence why he cant blow up the train, or even fight back. the fact neo ended up in this area via the "real" world proves that the real world and the matrix are all within each other, how else would neo end up in the matrix without jacking in? he ended up where he did, because in shock of what he did, his mind refused to recognise the matrix or zion, and he ended up in the input loading area, the highest level of consciousness before waking up for real real.
He re enters the matrix with the aid of trinity, making the french men, download neo back. (the train,) neo returns, but knows some truths now he will not reveal to anyone else, (why he went away to think) he realises, that zion has a real worth, as it is humanities refuge of free thought, he also knows that defending zion is pointless, but he also realises that if smith corrupts the entire system, no more zions will ever be made, as if the matrix crashes, the humans in the batteries will quite likely end up brain dead,(killing the humans weakening the machines) he also realises the only way to save it is to make a deal with the main computer system, by defeating smith, as he is the only thing without restraints that can defeat smith, the main computer system will not repeat the mistake it made with smith, ie allowing another program as much power, so it knows neo is the only solution, but in a way neo does not yet know, so neo goes off to fight smith, in the one place he can kill him, deep in the internal software of the main computer system.
Neo and smith fight backwards and forwards, but they are balanced equations, neither can ever win over the other, they are too evenly matched, neo realises this when the oracle says through smith, "everything that has a beginning has an end" neo then realises the truth, smith will exist as long as neo exists, a program with no purpose is deleted, and with neo dead, smith has no purpose, neo allows smith to kill him, and then smith is a slave to his origional programming, and is deleted.
Why did some programs help the humans? I believe the oracle was trying to preserve zion, as her purpose was to moniter zion and the matrix, if the matrix and zion had been destroyed, then her purpose would have been removed and she would have been deleted, so she was in it for self preservation, as were her security protocals. the architect said "she had played a dangerous game" ie she had helped the humans to prolong her existance, the architect however was not as worried as he existed outside the matrix, (where the parents on the train came from). however it was in his interest that neo removed smith, and also that neo was removed, the matrix could then return to normal, and become relatively ordered again, avoiding the crash, and avoiding the loss of batteries that would have resulted.
So zion was saved, and it was worth saving, as at the end of the day, freedom is freedom of the mind, doesnt matter if your body is imagined.
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