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If an Agent can possess anyone still connected to the Matrix, and, as we can see, they sense when someone is seen something weird (like the drunk beggar in the first movie), why didn't they possess Neo when he was in the car with Switch Apoc and Trinity?

I believe that's what Trinity meant when she said the gun was for their protection from him

Neo: what is this? (talking about the gun pointed to him)
Trinity: It is necessary, for our protection.
Neo: From what?
Trinity: From you!

LcSalazar
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    I thought that comment was more about the fact that he was still an unknown quantity at that point. They had no idea if he could truly be trusted, or if he would have a mental breakdown, or whatever. – phantom42 Nov 24 '14 at 14:54
  • My answer to "What was the point of the bug?" explains this. – Null Nov 24 '14 at 15:03

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