Architect: You have many questions, and though the process has altered your consciousness, you remain irrevocably human. (M2)
Many believe "the process" refers to Neo's entire life and development as the One, but the Architect's statement about "the process" is too vague and would be too confusing to Neo at this point if it were the case. There is no reason for the Architect to believe that Neo would understand what he means by "the process" if he is indeed talking about the "process of the One". Neo doesn't even understand that the One is part of the system yet. This makes no sense in the context of where the conversation is at this point.
Instead, I think "the process" refers to the process that Neo's consciousness went through to get from the Matrix to the Architect's TV Room construct. This process happened only seconds ago and is surely one of the first things Neo is wondering about, and this would make much more sense in the context of this conversation which has just barely begun. So, what part of Neo's consciousness did this process alter?
Notice that all three of these "alterations" to Neo's consciousness make Neo more like a machine or program and thus less "human". This gives even more meaning to the Architect's phrase, "irrevocably human". Despite all of the changes the Architect has made to enhance Neo's consciousness, there's nothing the Architect can do about Neo's unfortunate human identity.
There is another huge piece of evidence that validates what the Architect means by "the process". Remember in M1 when the sentinels flew by the Nebuchadnezzar and the crew turned the ship off so the sentinels wouldn't see them? Neo did not "feel" the sentinels at that point. However, in M2, after Neo chooses the left door and saves Trinity, the Nebuchadnezzar crew detects sentinels that are staying outside of EMP range. Nobody knows why. But somehow, even before the sentinel starts twirling in order to send the bomb their way, Neo knows the intentions of the sentinels, and he tells the crew it's a bomb. After the bomb destroys the Nebuchadnezzar and the sentinels chase after the crew, Neo stops and says, "Something's different. I can feel them." Clearly, Neo did not have this sense in the real world until after his discussion with the Architect.
Many believe that Neo's real world powers are just another result of the anomalous summation that makes up the One. But this makes no sense, because by definition, anomalies are rejections of rules within the Matrix. The real world and the Source lie outside the realm of rules within the Matrix. And, just as there is no rule for which rejection of it produces perfectly accurate visions of the future, there is also no rule for which rejection of it produces an ability to destroy sentinels with mere thought or to see machines without using one's eyes. The Oracle tells Neo in M3 that the power of the One extends to the Source in the real world. Now we know that Neo gained these powers through the "process" he went through in order to escape the Matrix and enter the Architect's TV Room construct.
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