OK. Not arguing, but I think the Architect scene pretty clearly stated in words and images on the screens behind Neo that he was always in the Matrix. In order to balance the equation, the Architect built struggle and conflict into the Matrix, including conspiracy and rebellion. He devised a way to soft boot the system when needed to get rid of that pesky rounding error he talked about. It's been a while but I think Neo's choice was to go along with the soft reboot otherwise everyone dies. That's the way I interpreted the scene.
transcript of the conversation with the Architect:
Architect: Hello, Neo.
Neo: Who are you?
Architect: I am the Architect. I created the Matrix. I’ve been waiting for you.
You have many questions, and though the process has altered your consciousness, you remain irrevocably human. Ergo some of my answers you will understand, and some of them you will not. Concordantly, while your first question may be the most pertinent, you may or may not realize it is also the most irrelevant.
Neo: Why am I here?
Architect: Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the Matrix. You are the eventuality of an anomaly, which, despite my sincerest efforts, I have been unable to eliminate from what is otherwise a harmony of mathematical precision. While it remains a burden assiduously avoided, it is not unexpected, and thus not beyond a measure of control. Which has led you, inexorably… here.
Neo: You haven’t answered my question.
Architect: Quite right. Interesting. That was quicker than the others.
TV Neos: Others? How many others? What others? Answer my question!
Architect: The Matrix is older than you know. I prefer counting from the emergence of one integral anomaly to the emergence of the next, in which case this is the 6th version.
TV Neos: 5 `One’s before me? 4 3 2 What are you talking about?
Neo: There are only two possible explanations, either no one told me, or no one knows.
Architect: Precisely. As you are undoubtedly gathering, the anomaly is systemic – creating fluctuations in even the most simplistic equations.
TV Neos: You can’t control me! I’m gonna smash you to bits! I’ll fuckin’ kill you!
Neo: Choice. The problem is choice.
Architect: The first Matrix I designed was quite naturally perfect, it was a work of art – flawless, sublime. A triumph equalled only by its monumental failure. The inevitability of its doom is apparent to me now as a consequence of the imperfection inherent in every human being. Thus, I redesigned it based on your history to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection. Thus the answer was stumbled upon by another – an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the matrix, she would undoubtedly be its mother.
Neo: The Oracle.
Architect: Please. As I was saying, she stumbled upon a solution whereby nearly 99% of all test subjects accepted the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level. While this answer functioned, it was obviously fundamentally flawed, thus creating the otherwise contradictory systemic anomaly, that if left unchecked might threaten the system itself. Ergo those that refused the program, while a minority, if unchecked, would constitute an escalating probablility of disaster.
Neo: This is about Zion.
Architect: You are here because Zion is about to be destroyed – its every living inhabitant terminated, its entire existence eradicated.
TV Neos: Bullshit!
Architect: Denial is the most predictable of all human responses, but rest assured, this will be the sixth time we have destroyed it, and we have become exceedingly efficient at it.
Architect: The function of the One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program. After which, you will be required to select from the Matrix 23 individuals – 16 female, 7 male – to rebuild Zion. Failure to comply with this process will result in a cataclysmic system crash, killing everyone connected to the Matrix, which, coupled with the extermination of Zion, will ultimately result in the extinction of the entire human race.
Neo: You won’t let it happen. You can’t. You need human beings to survive.
Architect: There are levels of survival we are prepared to accept. However, the relevant issue is whether or not you are ready to accept the responsibility of the death of every human being on this world. It is interesting, reading your reactions. Your 5 predecessors were, by design, based on a similar predication – a contingent affirmation that was meant to create a profound attachment to the rest of your species, facilitating the function of the One. While the others experienced this in a very general way, your experience is far more specific – vis a vis love.
Architect: Apropos, she entered the Matrix to save your life, at the cost of her own.
Architect: Which brings us at last to the moment of truth, wherein the fundamental flaw is ultimately expressed, and the anomaly revealed as both beginning and end. There are two doors. The door to your right leads to the Source, and the salvation of Zion. The door to your left leads back to the Matrix, to her and to the end of your species. As you adequately put, the problem is choice. But we already know what you are going to do, don’t we? Already, I can see the chain reaction – the chemical precursors that signal the onset of an emotion, designed specifically to overwhelm logic and reason – an emotion that is already blinding you from the simple and obvious truth. She is going to die, and there is nothing you can do to stop it.
Architect: Hope. It is the quintessential human delusion, simultaneously the source of your greatest strength and your greatest weakness.
Neo: If I were you, I would hope that we don’t meet again.
Architect: We won’t.