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Originally posted by Nappa
Two thing I didn't understand about the film :
First, if Neo's design/purpose as the "One" is to restart the Matrix and erase the "anomalies" within the program, then why do Agents try and stop him and the others? The Agents obviously take orders from somewhere, but why would the machines want to see Neo killed? Wouldn't they be ordered to HELP him? Perhaps the Architect has kept the other machines in the dark about the Neo flaw?
Also, at the end, has the matrix been destroyed? I thought the door Neo chose would crash the system and kill EVERYONE in the pods, but they never mentioned it afterwards. Sooo, the only people left are those in the "Zion Matrix"?
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At the end of the movie the matrix still hasn't been destroyed yet, it ends only a few minutes after Neo chooses his path. We will find out in Revolutions what actually happens because of Neo's choice.
As for why the agents try to stop Neo: Because they know that as hard as they try they really can't stop him. Basically they are there so that Neo can "discover" his purpose in life. Something he can't do if the agents are helping him.