In the beginning, there was the Second Renaissance (see Animatrix). The Architect created the Matrix to place the minds of the subjugated humans. "It was a work of art...flawless, sublime. And triumphed equally only by its monumental failure." The Oracle is a lesser program to the Architect. Whereas the Architect sought perfection, the Oracle realized that the human mind couldn't accept such a utopia. The human mind couldn't accept a reality that was forced upon them, it had to choose to accept that reality, even if that choice was at a subconscious level. Thus the Oracle created the first functioning Matrix. Choice was given to the populace of the Matrix at a subconscious level. "While this answer functioned, it was obviously fundamentally flawed…" The choice made the equation unbalanced, meaning that while 99% accepted the Matrix, 1% would still make the choice to get out. That 1% is allowed to leave the Matrix and reside at Zion. The remainder of the unbalanced equation eventually will add up such that eventually, the ONE is created.
The ONE has enormous powers within the Matrix. Think of an equation where the sum of the remainders eventually gets large enough to affect the outcome of the equation. This of course would make the equation even more unbalanced, leading to a cataclysmic system crash if not corrected. In order for the Matrix to continue, the ONE has to remake the choice for everyone to stay in the matrix (rebalancing the equation). However, this leaves out the people living in Zion. If left to their own devices, they will only grow stronger and attack the machines again. With the emergence of the ONE, the people of Zion is no longer necessary and can be destroyed. The ONE then choose from the matrix 23 individuals--16 females, 7 male--to rebuild Zion, thus preserving the mythology. This has gone on for 5 cycles.
The Oracle became impatient.
The existence of this cycle means the war of humans against the machines never really ended. There will always be battles fought in a never-ending cycle.
The Oracle is frustrated.
She came up with a scheme to force a truce, a cease-fire between the humans and the Matrix. This is not an easy task. The machines obviously have the upper hand. They completely control the humans, and have a working system ensuring that relationship of master and slave never changes. The humans will always have renewed hope and choice in their futile battle against the machines, but they will never even come close to having a bargaining chip with the machines for peace. In order for there to be peace, the machines have to need something from the humans. But what? The machines are willing to accept a level of survival where the human race is extinct. The machines were able to survive for the period after the sky was darkened, but before they had control of the humans. They know they can survive without the humans. What possible bargaining chip can the humans have to use against the machines? Something has to change.
The people who made the choice to leave the Matrix made that choice when they were relatively young, teens and below. The 5 previous ONE are no exception to the rule. They would have no real life experiences inside the Matrix; their formative years are spent inside Zion; they will have known only war against the machines to save humanity. All this was meant to create a profound attachment to humanity. When finally called upon to make the choice for humanity, the ONE would inevitably choose to save humanity over Zion, his life experiences will have formed him in such a way to choose the needs of the many over the needs of the few. This was by design.
Neo was not released from the Matrix until his mid to late 30s. Quite possibly he has known love, or known the anguish of the lack of love. He is an adult. Adults are usually more selfish than children, and can be more irrationally emotional than children. (At least, in this movie they are.) The Oracle knows this, and quite possibly might have had a hand in hiding Neo for so long. The purpose of this is to facilitate Neo to reject the Architect's offer, the first step in breaking the cycle. Neo selfishly choose to save Trinity over humanity because of his love for her.
The second step is the creation of Agent Smith. It is obvious most/all agents are not aware of the grand design of the Architect's plan. Agent Smith didn't even know the location of Zion. Shortly after Neo escaped the Matrix, he learned enough of his abilities to destroy Agent Smith. Yet somehow he came back, more powerful than ever. Quite possibly the Oracle resurrected Agent Smith at this point, and made some altercations. She made Smith just as strong as Neo, but a polar opposite mentality. A virus, whose sole purpose was the destruction of anything he touches, including the Matrix.
This was the Oracle's gamble.
With control of the humans, the machines were free from risk. Even if humanity was destroyed, the machines would still be able to survive to a certain extent. However, Agent Smith actually threatens the Matrix, and the machines like never before. He is a self-replicating virus that cannot be stopped. Not only does he take control of human minds, but he can also control other programs as well, even one as powerful as the Oracle. Eventually he may even take over the Architect, thus rendering all of the Matrix and the machine world dead. The machine's level of security has been designed to keep the humans in check. The agents are more than capable of this task. The machines do not have any security to guard against an internal virus, especially one as powerful as the ONE. ...continued in the second column...
Thus was Neo able to get the bargaining chip he needed. Neo is now the only one capable of stopping Smith. The code that Neo carries is the exact opposite of the Smith code. Only by merging with Smith can he be destroyed, at the cost of Neo's own life. Knowing this, he was able to secure a cease-fire from the Machines, from the Architect. Finally ending the cycle of Zion.
Q and A on this theory:
Q: Why is Neo so powerful? What makes him different from other humans? Is he even human?
A: I believe he is human, although I don't think it matters in this context. Regardless of how he became powerful, he is, and by movie conventions the viewers should just accept that. The Architect did stress that the life of the ONE is the sum of the remainder of the equation. In the Matrix world, software code and the human mind are completely intertwined, indistinguishable from each other. For the people inside the matrix, there's a continuous interchange between the Matrix code, and their own mind. The creation of the ONE could just be as easy as this remainder getting inside the mind of the ONE, giving his code that extra value to win out above all other code inside the Matrix.
Q: If Neo had allowed himself to be taken over by Smith in Reloaded, could that have destroyed Smith?
A: yes. However, Smith had not become a threat to the Matrix yet, and Neo certainly hadn't tried to broker any deals with the Architect. So destroying Smith at that point would be useless. The ultimate goal is to end the cycle. Destroying Smith and Neo at that time would not only end the hope of humanity, but also unbalance the Architect's plan.
Q: How is Neo able to control machines in the real world?
A: Cinematically, it doesn't really matter. It's just a plot device to show his power. However, here's a possible explanation. Neo gained that power after having almost merged with Smith, after having been to the Architect's TV room, and after bringing Trinity back to life. The software of his mind had become intertwined with that of the Matrix. A possible theory then is that his mind has grown so in-tuned with the code of the Matrix that he can sense anything that bores that code. The squid robots, the buildings/machines of Machine City, etc. all should have similar basic underlining code, same language, platform etc. Losing his sight served to focus his mind even more to this link. It allowed him to "see" the Matrix code by shutting down one of his other senses (input). You can think of it as him having gained a 6th software sense, and that sense allowed him to not only receive (see) code, but also to send (command) code. I don't think he caused the squid explosions so much as he commanded them. He can't affect anything that wasn't built by the machines. He can't levitate a spoon let along bend one, but he can see the machine city even when he is blind.
Q: So where is this place between the Matrix and the real world?
A: It is yet another plot device. So here is yet another possible explanation. A lot of things happened during that time. Neo had just revived Trinity when they were attacked by sentinels. They abandoned the Nebuchadnezzar, and that's when Neo started to be able to "feel" the sentinels. It is possible that while reviving Trinity, Neo got really in close to the Matrix code. When he came out, he was disoriented. He was having trouble telling apart the difference between the real world and the Matrix code he is starting to sense in his new 6th sense. That's when he went into the coma. The train station can possibly be thought of as a temporary folder, an emergency backup of the latest version of a code/document. Morpheus and Trinity had to go and retrieve this bit of code to reload back into Neo's mind. What they probably did (but didn't show 'cause it's not necessary) is to plug Neo back into the Matrix, and dial in on a phone (connection) they have access to. That can reload this backup into Neo's mind, and wake him from his coma. Yes, this is very weak, but then again, it was a stupid plot device to begin with.
Another possible explanation. At this point, his 6th sense, his "software sense" is just starting to grow. Obviously he can't control it yet, he just knows that something is changing. So when the squid came upon them, in his attempt to send the stop command (instinctively), he accidently sent a bit more than he should have. He sent part of himself back into the Matrix. That's the part that Morpheus and Trinity had to go back and rescue.
Q: If EMPs are the only thing that can destroy the machines easily, why doesn't the defense of Zion have a whole bunch of EMPs?
A: There are subtle hints that the ships used by Zion were built before Zion. The Nebuchadnezzar's plate said it was built in early 21st century. That would place it older than the first Matrix. During the preparation of the battle, it is also obvious that great value is placed on each one of these ships, and that there are very few of them. My guess is that Zion does not have the technology to build more EMPs. They are using existing technology either left over from the initial war, or allowed by the machines. Just enough weapons to keep themselves alive, but not enough to actually pose a threat to the machines.
Q: What about all the other side characters? The Indian Family, the Merovingian and Persephone, the Keymaker, the Trainmaster, etc.?
A: They are mainly plot devices that didn't figure in to the grand scheme of things. Details that tried to make the story more colorful, but ultimately made no difference to the story. Just like the cookies, candies, etc. The Indian family is there as an exposition device to let Neo know where he is and what's going on; the entire Merovingian sideplot is just a glimpse into how machines/programs can have their own agenda, and also a plot device for Neo to show off. If Neo had never meet the Indian family or Merv and company, the outcome of the story would not have differed appreciably. The End of this section
:ross: expression the whole time.
