Lets talk about the holes in the matrix movies here collectively.
1 that i found is that ..if NEO can stop the bullets then he should be able to stop other people in the matrix as well and in this way he can kill everyone in the matrix quite easily but he didnt. why?
i know this because Morpheus told our hero that there was one born in the matrix who could rewrite the matrix as he saw fit...Neo is the ONE, thus, he has the power to rewrite the matrix, thus, he wills the bullets to stop, however, i think he is still bound by the rules of the real world, the natural laws thus, he cannot make the bullets return to their origins with enough speed to do anything. I think.
either he has not been able to achieve this mindset, or even this is impossible for Neo...He can't rewrite EVERYTHING, otherwise he could just write himself as UberNeO and beat EVERYONE...it doesn't work that way, he has to struggle somewhat.
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yep the agent are there to kill the keymaker (aparently), yet as a causality they cant kill the keymaker, he cant die until he gives the one the key and its because thats the way it was programed to happen. Everything is meant to happen, everything is control!! except smith I think he really is a problem for the omnipotent figure (i think we are yet to meet)
Inside the Matrix, Neo is telekinetic, as seen when he summons the weapons off the wall in the mansion scene in Reloaded. So Neo most likely stopped the bullets telekinetically.
__________________ "The MTV Movie Awards are a systemic anomaly inherent to the programming of the Matrix. Although the transport process has altered your consciousness, you irrevocably remain human. Ergo, concordantly, vis-a-vis... You know what? I have no idea what the hell I'm saying. I just thought it would make me sound cool."
-The Architect AKA Larry