by Paul McCord
Thanks to Melloccino and everyone from alt.movies.the-matrix!

When first born, animals/humans undergo a process called imprinting, after which the newborn unmistakably recognizes the unique features of the first person(s) the child bonds with (usually the mother, followed by the father). Now within the context of The Matrix, consider what would happen if a program underwent an imprinting process with a human: they would recognize the code of the human above all other code (notwithstanding the code of the other parent). The program would be as fixed on the human parent as the eye of Sauron was on Middle Earth.

First, some contextual facts:

1. The prophecy states that a man would be reborn inside the Matrix, a man who could rewrite contents of the Matrix as he saw fit.
   
   
2. At the end of The Matrix, Neo destroys Smith, but he is quite obviously alive and well in Reloaded and Revolutions, begging the question: Why? What follows won't be easy to swallow, but I promise it is the truth.
   
   
3. In Reloaded, just before the Neo versus 100 Smiths battle, Smith tries to explain to Neo the connection between them ("...some part of you imprinted onto me, something overwritten or copied..."). Smith later admits that he has become "a new man, so to speak" because of Neo. (The full line is: "I stand because of you, Mr. Anderson. Because of you I'm no longer an agent of the system. Because of you I've changed. I'm unplugged; a new man, so to speak; like you, apparently free.")
   
   
4. In Revolutions, just before Smith assimilates the Oracle, she says to him, "You are a bastard," to which Smith replies, "You would know, Mom." This was the straw that broke the metaphorical camel's back for millions of Matrix fans, at least those who even watched the third movie after the confusion of learning that the prophecy was a lie in the previous movie.

But not to worry -- let's put the pieces together.

Smith is quite obviously reborn after Neo destroys him at the end of the first film. According to the rules of the system, Smith should have been compelled to report for deletion, but he "didn't", he "couldn't." He "was compelled to stay, compelled to disobey" -- exactly the opposite of what a true agent would feel, but exactly what a believer in the autonomy of the human soul like Neo would believe. And here's the punchline: imagine Neo saying, "Smith, I am your father," because after Smith's rebirth, that is exactly who Neo is. Smith inherited his individualist, autonomous ways from the one he was sworn to kill, and for that reason he was drawn to him, fixed on him ... like the eye of Sauron fixed on Middle Earth.

But if Neo is the (artificial) father, who is Smith's mother? The Oracle, of course. She is the mastermind who created this game, and from the first time she met Neo in her kitchen, she knew who he was -- the carrier of the code of the systemic anomaly -- but she also knew who he was not -- the One. Neo was not the One.

But if not Neo, who was the One? Let's consider the prophecy again: "When the Matrix was first built, there was a man born inside who had the ability to change whatever he wanted, to remake the Matrix as he saw fit... After he died the Oracle prophesized his return and that his coming would hail the destruction of the Matrix, end the war, bring freedom to our people."

I can see the truth is becoming clearer to you now. Neo was never "born inside" the Matrix. He was born outside, in the machines' human-harvesting power plant. However, following his destruction at the end of the first movie, Smith was born inside the Matrix -- he was truly "born inside" -- the product of the Oracle's programming (hence "Mom") and Neo assimilating him. Neo's human code, systemic anomaly and all, had combined with what Smith had been to give birth to a man, the new Smith.

Still need convincing? What happened at the end of Revolutions? Smith, who had avoided returning to the Source when he chose exile upon his rebirth, never considered that Neo had been uploaded into the Matrix directly from the machine city ('01'). As soon as Smith's assimilation of Neo was complete, Smith -- The One -- was connected directly to the Source. His code was then disseminated, and the prime program was reinserted, allowing the Matrix to be reloaded. Combined with Neo's deal with Deus ex Machina, this ended the war and brought peace to the people of Zion.

And to think, we all have the Oracle to thank. She deceived everyone -- Neo, Morpheus, us! To what extent she deceived her program and machine counterparts we may never be sure, because although Seraph, the Keymaker, the Merovingian, and the Architect all refer to Neo as "The One" at some time or another, they could all have been deceived by exactly who or what The One really was, and some (such as Seraph) could just as easily have been playing along with the Oracle's deception. After all, if you recall the Architect's scoffing at the Oracle in his speech in Reloaded, even he acknowledged that it was she who developed the systemic anomaly. Thus, only she knows its true nature.

She wouldn't be much of an Oracle if it were any other way!