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When Morpheus has Agent Smith pinned to the ground, he asks "and you are?".....which to me obviously means he does not know this Agent. Surely he knows their names if the Agents have been pursuing them for some time. Smith is even in the construct. Morpheus behaves like he has never seen Smith before.

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Agent Smith establishes that he is a unique and different agent when he sends the other two agents while interrogating Morpheus. He pulls off his shades and removes his earplug as an indication that he is speaking for himself, not as an Agent, as depicted in the first few seconds of this video:

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Before Morpheus met Smith, he knew Agents only as anonymous programs with a specific purpose. Agent Smith was something new--an Agent with his own goals and desires. As such, he was someone--something--that Morpheus had never encountered, and never imagined.

  • I suppose so. I just thought that Morpheus had not been captured before, so yea he obviously wouldn't be aware of Smith's personal interests and unique individualistic ways. I just thought as an Agent himself, Morpheus would have been aware of his name. He becomes aware of Smith as an individual when Smith removes his glasses and earpiece. – Cake_Badger Oct 2 '16 at 15:49
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    Oh, Morpheus had never been captured before--it was established earlier in the movie that no one who had been captured had ever escaped. – Justin Eiler Oct 2 '16 at 15:50
  • But would the crew being lead by Morpheus know the Agents names? – Cake_Badger Oct 2 '16 at 15:53
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    I don't recall any references to Agent's names from the the crew--and I had always understood that to the folks from Zion, the Agents were not identifiable individuals. This may be an error on my part, but I believe that the people of Zion saw the Agents as largely anonymous and interchangeable. – Justin Eiler Oct 2 '16 at 15:56
  • The scene in your answer occurs after the scene in the question, though. Morpheus wouldn't have viewed Agent Smith as special in any way when he asked him "and you are?". The fact that the scene in your answer is part of an interrogation also means Agent Smith is more likely to be lying or acting differently in order to break Morpheus. – Null Oct 3 '16 at 17:17
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I feel like this is pretty expressly conveyed from the beginning of their conversation.

Smith: The great Morpheus. We meet at last.

Morpheus: And you are?

Smith: A Smith. Agent Smith.

Morpheus: You all look the same to me.

The Agents are not people, but constructs. Smith isn't "Mr. Smith the Agent;" he's "A Smith." He's not an individual, he's a template. He is one of many Smiths.

And they all look the same to Morpheus.

Edit to add: But at the same time, the agents are all networked. So Smith knows everything about Morpheus that any other agent knows.

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It's clear that Morpheus and Agent Smith had never met in the Matrix before:

Agent Smith: The great Morpheus. We meet at last.

Morpheus: And you are?

Agent Smith: Smith. Agent Smith.

Morpheus: You all look the same to me.

Morpheus is unlikely to know Agent Smith's name even if the two had run into each other in the Matrix before because (a) Agents' names don't matter and (b) Zion operatives run from Agents and rarely have much of a chance to talk to them anyway.

The fact that Morpheus and Agent Smith had never met before may initially seem surprising since:

  1. To the Agents, Morpheus is a notorious criminal who has surely encountered Agents before. Furthermore, we only see three Agents in The Matrix (Smith, Brown, and Jones).
  2. Agent Smith's face is seen in the Agent training program (as you pointed out).

Although we only see three Agents in The Matrix, there are actually over a dozen named Agents in the universe of The Matrix as well as some unnamed Agents (e.g. in Beyond from The Animatrix). Consequently, it is entirely possible that Morpheus had been pursued by other Agents in the past but never by Agent Smith himself.

As for why Agent Smith's face is used in the Agent training program, recall that there are other Zion hovership crews hacking into the Matrix (we see several such crews at the Crisis Meeting in The Matrix Reloaded). Some of these crews likely encountered Agent Smith, and during any such encounter the code for Agent Smith's "face" would have been captured by the hovership's operator for later use in the Agent training program.

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