I think a lot of you have missed some of the much deeper underlying biblical connections of this trilogy. All the answers you seek are there, but not smashed against your nose so that you're sure not to miss it. Personally, I feel the entire Matrix trilogy is an incredible piece of literary science fiction. I really enjoy discussing these movies, so by all means ask questions and slam my opinions back in my face. That's where the fun lies. However, I ask that you do so without personal attacks, there's no point in responding.
The entire Matrix trilogy really ties in closely to western religion. Each character can be considered a counterpart from religious texts. The Architect for example would be God. He's created an Eden for the humans to live in. Consider a quote by Agent Smith, "the first Matrix was designed to be a perfect human world. Where none suffered. Where everyone would be happy." However, humans demanded the ability to choose. They wanted free will. They chose to cast themselves from the Garden and live in the much dirtier, hard world full of suffering and imperfection. I.E. they take the 'red pill' and are removed from Eden.
Eventually the humans decide they can wipe out God by blackening the sky. However, as we know, the humans lose the war and are cast aside. Several versions of the Matrix are attempted, but all are refused by the humans. Finally one edition of the Matrix is designed to allow the Humans to grow, or choice. The machines don't understand this growth and fight it. When designing the third Matrix, referred to as 3.0, the Oracle realizes that this growth will eventually give humans the ability to cross the Matrix and the Real World. She however, sees this ability as a benefit to both man and machine, as this is the only way the machines will learn to evolve. By combining both man and machine, it will bring the machine evolution that is required.
Now enters Neo 1. He chooses to give rebirth to Zion, or chooses the door to the right. Thus the cycle of previous Neo's begins. They go through 5 before we get to our current Neo. Here are some quotes from the Architect scene in Reloaded.
Quote:
Architect - You have many questions, and although the process has altered your consciousness, you remain irrevocably human. That was quicker than the others. While the others experienced this in a very general way, your experience is far more specific. Vis-a-vis, love. I prefer counting from the emergence of one integral anomaly to the emergence of the next, in which case this is the sixth version. The Mother stumbled upon a solution whereby nearly 99.9% of all test subjects accepted the program, as long as they were given a choice.
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Quote:
Neo - Choice. The problem is choice.
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The mother he refers to is the Oracle. She's found what it is that the humans need in order to accept their reality, however, it also what will eventually lead to the end of the war and bring humans and machines back together. Each Neo has learned and grown slightly from the previous, until our Neo chooses Trinity. Instead of rebirth again for Zion, he chooses the door on the left. Thus the Revolution begins.
Where Neo is the saviour of humanity, Smith could also be considered the same for machines. As Neo realizes his ablitity to cross the gap between humans and machines, Smith also learns this ability though from machines to humans. Thus is why he's able to tap into the human form and take over Bane's body. This also explains why Neo is able to see the machine's as the light in the real world. They've begun the crossing of both planes, that eventually leads to the coexistence of humans and machines in the end. However, Smith also learned how to grow similar to humans. Beforehand, machines were uncapable of this growth. They worked in a simplistic perfection, fullfilling only the purpose of their existence. Because of this Smith becomes the virus of the machine world, spreading thoughout and threatening the future exsistence of the machines. Because of Neo's ability to cross the machine and human world, he lead Smith to a point that the machines were able to destroy him permanently. Thus is what happens at the end of Revolutions, through Neo the machines destory the virus Smith has become.
I read a lot of you complaining about the child that's prevailent through the movie. She too is a symbol of the future coexhistence of machines and humans. The machines didn't understand love on a human level, but as the program (the father of the child) revealed, they understood the connection between two programs. Thus this is the first child born of a human understanding. She serves no purpose, thus is why she's subject to deletion. Remember, the machines serve only their purpose, they don't grow or evolve. To save his child, the father has her trancend the machine world and the matrix via the frenchman and the train station. He's basically smuggling her inside where she'll be safe. This child is the 'last exile' because of her 'birth' via two programs who created her via a human trait. Thus the child herself is basically human.
The conclusion of the film was the perfect ending in my opinion, to what's to happen in the future for man and machine. The humans will be freed.
Quote:
Oracle - Will you free the others?
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Quote:
Oracle - Do I have your word?
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Quote:
Architect - What do you think I am, Human?
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This ending also leaves the assumption that eventualy this coexistence will wear thin. More than likely another form of the Matrix will be redeveloped and another annomoly, probably Neo from the Oracles quote about seeing him again, will rise and the cycle will begin again. Definitely leaves another movie or more open for the future.