A reader of this website wrote in:
After Neo's conversation with the Architect, Neo is asked by Morpheus how he knows the war will be over in 24 hours. Neo answered that he was told it would happen. it doesn't matter by whom - he believed him. Did Neo ever tell anyone about the Matrix system? And above all, why didn't he tell them at that point?
When Neo says, "it doesn't matter by whom," Neo is of course referring to the Architect. He almost certainly withholds this information out of fear that the people around him might distrust him more if he explains just how much a part of the system Neo was created to be. Neo was designed to enter the Source, talk to the Architect and start the next Matrix iteration, so even if Neo personally rejects this function/duty with every fiber of his morality, letting Zionists know about how the Matrix system works would also mean letting them know that he himself is part of that system, which might have even landed Neo in a Zion prison just to protect Zionís safety. (Surely Commander Lock would have proposed throwing Neo in jail if only he had known machines purposely designed Neo to be the One.)
There was a conversation in M2 that supports this:
Neo: I just haven't been able to sleep much.
Counselor Hamann: It's a good sign.
Neo: Of what?
Counselor Hamann: That you are, in fact, still human.
There are many ways this could be taken, but Iíve always heard this as Councillor Hamannís way of saying, ďI hope you actually are a real human and not part of the machinesí plan to destroy Zion.Ē That same conversation ends with the counselor saying:
"I have absolutely no idea how you are able to do some of the things you do, but I believe there's a reason for that as well. I only hope we understand that reason before it's too late.
Again, this sounds to me like he is hoping Neo isn't knowingly or unknowingly acting (or going to act) as a weapon for machines.
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