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I've been rewatching parts of The Matrix because of the questions I've been asking. Maybe this is in a scene I haven't re-watched, but I don't remember it being covered in the movies.

If an Agent takes over a person's avatar in the Matrix, what happens to that person? When the agent leaves, do they return to their normal routine? Are they given manufactured memories? Or is there too much to patch up so the Matrix has to make the person into a murder victim? And if the Agent is killed (which wasn't considered to be a problem until Neo came along), is the person who was replaced also killed?

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    The better question is what happens to the real life humans when their matrix counterpart is taken over by the agents. when killed? – user6117 May 2 '12 at 7:01
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There was at least one on-screen instance of an agent being killed in action - In the "Dodge This!" scene, one of the Agents takes over a helicopter pilot and, eventually, is shot by Trinity. The agent reverts back to the pilot, dead. So if an agent dies in a host, the host does die.

As for an agent willingly leaving a host, I'm fairly certain that's not in the three movies (or the one movie, depending on who you ask). My educated guess is that the time would just be blacked out. You see that all over sci fi when someone is being possessed. [Richard's middle example supports this].

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    Note: There are a few examples where Agents can be presumed to have willingly left their host (I remember at least one chase scene, in the first movie, where Agents seemed to only briefly occupy some individuals) but we never see what happens when they leave because that occurs off-screen. – Iszi Mar 18 '12 at 5:45
  • Most likely, the person taken over will be stuck in a loading screen/lag spike. – krillgar Nov 29 '14 at 12:04
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There are three fully canon examples of an Agent leaving a 'civilian' after possessing them.

Animatrix canon.

In the Animatrix segment "Detective Story", Trinity shoots a private detective who's just been taken over by an agent. No sooner has he been shot then the agent leaves (to find a less disabled host) and he is restored to his former self with no obvious ill-effects aside from the fatal gunshot wound.

Webcomic canon.

In the comic "Day in...Day out" which you can read online here, a civilian is taken over by an agent. After an extensive firefight (in which 'Agent White' loses an arm) she is restored to her body and has no memory of the incident but still has the injuries suffered during the assault.

Day in, Day out webcomic

This is extremely similar to the comic "Wrong Number". An Agent takes over a telephone repair engineer and kills a redpill, then regains consciousness with no memory of having been possessed.

enter image description here

Film canon.

The last instance offers no clarity as to the mental state of someone being left by an Agent but when Trinity shoots the helicopter pilot (in the famous "dodge this" sequence), we see the pilot revert to his former self physically within seconds. The agent reappears a few minutes later, after having possessed another human.

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