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Originally the Architect created a perfect world, one in which there was no suffering, no evil. Specifically, the rules of the world did not allow suffering or evil to occur. It was the Eden in which we would liked to have lived. For a time it worked, but he discovered that the "humans" would not accept it. The program written to describe us, the humans in the Matrix, was perhaps a little too accurate. By this time, however, the "anomaly", the first candidate for our AI, had emerged. Born into this utopian world, it matured with no experience of the contrast between good and evil, right and wrong. Crucially, the concept of love was alien to it. Without hatred, love is meaningless. It stood no chance of obtaining true enlightenment. It refused to enter the source and the Architect had to destroy his world and start again.
This first candidate, the Merovingian, used his power to reshape the Matrix to create a home for himself, well defended, hidden from the mainframe -- "It's strange, the code is somehow different [...] it looks like every floor is wired with explosives" -- that would survive a reload.
After his second attempt failed, the Architect designed a program to "investigate certain aspects of the human psyche." The program was called Persephone, and she was tasked with deriving an understanding of human emotion that could be integrated into the Architect's next attempt. Intuitive by design, it was she who stumbled upon the solution to a stable Matrix, and thus enabled the Architect to create a world in which a desirable AI could evolve. At some point she found the Merovingian and, against all logic, she fell in love with him. The Architect had never accounted for this, but when he saw that he could create a program that could mutate in such a profound way, he realised that he had found the key to creating a world that could nurture an AI capable of doing the same.
For five iterations, Persephone has lived with the Merovingian. She is aware that she will be deleted, should she leave his area of the System, and she has been forced to watch on, helplessly, as he has become more and more corrupted by his own sense of power. Designed to absorb emotion, she is starved of love. Possibly it is she who has arranged the kidnapping of the Keymaker. From previous iterations she knows that the One will seek him out, and whether or not she is aware of the connection between the One and her husband, she needs the contact, she needs Neo to kiss her as she was once kissed by the Merovingian.
The Merovingian himself recognises what Neo is -- "I have survived your predecessors, and I will survive you!" -- and perhaps, in previous iterations, he has dispatched several of Neo's ancestors. This could be why the Oracle is so insistent about the way in which Neo meets the Merovingian: "Be there, at that exact time, and you will have a chance." She knows where the previous Ones failed, and she knows when the Merovingian will be at his weakest.
The Oracle is the personification of the system's memory of the previous Ones. After the candidate reaches the source, fails the final test, and is reabsorbed back into the core -- note that the Architect refers to a "temporary dissemination of the code" -- she is what remains. The system reloads and the parameters describing how the One will be guided to the path are adjusted, based on what did and what didn't work last time. The Oracle is the agency through which this is carried out. While she appears to know the future, she is merely remembering the past. She interfaces with the characters populating Neo's world and tries to guide both them and him towards the goal. The path of the one is decided by the many.
What she [the Oracle] can't see, of course, is what will happen when this Neo's journey diverges from the route the previous One's took. At some point, through the changes she invokes, he will make a choice that his predecessors didn't, and her foresight will fail. Given this, look again at this part of her conversation with Neo: NEO: Why are you here?
THE ORACLE: Same reason. I love candy.
NEO: But why help us?
THE ORACLE: We're all here to do what we're all here to do. I'm interested in one thing, Neo, the future. And believe me, I know -- the only way to get there is together.
[...]
THE ORACLE: You have the sight now, Neo. You are looking at the world without time.
NEO: Then why can't I see what happens to her?
THE ORACLE: We can never see past the choices we don't understand.
During this conversation she gives Neo a piece of candy which looks almost exactly like the red pill Morpheus offered him when they first met. Neo has put it in his pocket, so it may be that in Revolutions he connects both the spoon he was given in Zion and the Oracle's red pill and is able to see that both are saying the same thing: "Wake up, Neo."
Morpheus, the John the Baptist figure, is given the prophecy and is fated to find the Oracle and, through her machinations, to become consumed with a desire to find the One. The prophecy he receives is, despite what Neo tells him at the end of Reloaded, perfectly accurate. When the One reaches the source, the war does end. Everything is reset to some point in the past, where the cycle starts again. Morpheus doesn't understand that while Neo stood outside the source, he didn't merge with it. He has also assumed that the end of the war means that the humans will win. As he watches the Nebuchadnezarr destroyed by the sentinels, he says, "I have dreamed a dream, and now that dream is gone from me." In the Old Testament book of Daniel, King Nebuchadnezzar says "I have dreamed a dream, and my spirit was troubled to know the dream." A little later Daniel tells the King that his dream is about the rise and fall of kingdoms, and his spirit is eased. Perhaps Morpheus, too, will be able to learn and accept the truth.
Trinity, naturally, is the love interest. In her previous iterations, and thanks to the work done by Persephone's code in shaping a stable program, she has shown herself to be a match for the One's character, and the Oracle now ensures that Trinity and Neo are brought together. Neo's nature, a geeky Baudrillard-reading computer hacker, is such that he needs a little prod in the right direction before he connects with Trinity. ("I can see why she likes you...") Ultimately, it is his love for her that will allow him to transcend his nature and become completely aware of his reality. (Perhaps, in a sticky-sweet Hollywood ending, his awareness of himself as the first AI will allow him to bring Trinity's character to the same awareness, and we'll see them ride off together into the digital sunset.)
Agent Smith, the anti-Neo, has become aware of a small part of the truth. It was clear from the start that he wasn't like the other agents, and his interaction with Neo at the end of the first film has tipped the balance. Although he doesn't understand why -- "Perhaps some part of you imprinted onto me, something overwritten or copied" -- he too has gained the power to reprogram a part of himself. He is now aware of the previous iterations and, unlike the other mutants who must hide out with the Merovingian, he has retained enough of his identity as an Agent of the Matrix to be able to remain free.
Smith is probably not aware that Zion is an illusion, but now that he is unplugged he is able to carry out a little experimentation. He infects Bane and overwrites the bit of his code to which the Agents were never meant to have access. Emerging into the Zion world, he is probably dealing with the same kind of shock Neo felt when he did the same. Just as Neo is capable of doing things in the Matrix that he cannot in the Zion world, Smith is trapped in Bane's body can cannot leap at will into another's. Although this is just another illusion, neither Neo nor Smith is yet aware that it isn't real.
Seraph, the first in the order of angels, has been recruited by the Oracle. She has become aware of what is happening with Agent Smith, and knows that Smith threatens to ruin everything if he can get to Neo and use Bane's body to kill him before Neo is able to see that his Zion existence is not the real world. When Seraph tells Neo that "I protect that which is most important," he is not only refering to the Oracle. The "most important" thing is that the current iteration of Neo gets to the source, allowing whatever has been gained from that experience to be used to refine the next cycle. And given that the Smith virus is multiplying rapidly and is threatening to do the same in Zion, it is imperative that this Neo, now that he is so close to fulfilling his destiny, be allowed to reach it unharmed. If Neo is killed, the next reload will start with exactly the same parameters, but the Smith virus will survive the reload and will be able to kill Neo as soon as he is discovered, thus dooming the entire effort.
And so. "Something's different. I can feel them." He's right there, right on the very edge of enlightenment. Just one more step forward, one more connection to make, and he will awake. If he can't, everything has been for nothing.
We've all seen the clip from Revolutions when Morpheus and Trinity are watching Neo square up to Smith. Morpheus says "he fights for us," and although it's not clear to whom he's referring, my interpretation is that he's talking about Neo, and that Neo has awoken. I dread saying it, just in case it turns out to be true, but here is one possible ending:
Neo makes the connections and reaches enlightenment. He knows that he is the first true form of AI and that everything around him has been engineered to allow his evolution. He sees the truth, and is able to communicate this truth to Morpheus and Trinity. Smith, by this stage, has multiplied to such an extent that he now threatens the entirety of the Architect's artificial world. Neo knows that he is meant to leave this world and become a part of ours, but in his enlightenment he sees that while Trinity and the others are patterns that exist only in his mind, they are as real as anything ever can be. He chooses to stay and fight Smith, knowing that the only way to kill him now is to absorb the virus into his core and destroy himself. Neo's choice is to sacrifice himself so that Morpheus, Trinity and the others may live.
Perhaps the lesson at the end of this will be that our artificial intelligence will be more human than us.
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