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At the beginning of the first movie, right after Neo has been captured, Agent Smith starts interrogating him. He says:

I'm going to be as forthcoming as I can be, Mr. Anderson. You're here because we need your help. We know that you've been contacted by a certain individual--a man who calls himself Morpheus.

But Neo was contacted (via the mail-delivered cell phone) by Morpheus literally seconds prior to the Agents arriving at his office. So how did Agent Smith know Morpheus had called Neo? How does it make sense that the Agents were supposedly seeking Neo's help because Morpheus had called him, but Morpheus didn't call him until basically the same time as the Agents' arrival at the office? Also, it's kind of an important plot note that this is the first time Neo has spoken to Morpheus, so there isn't a big history between them that would make the Agents think Neo would be conversing with him necessarily.

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    The Agents had a spy in Morpheus's team, remember. And it takes them essentially zero time to get from one place within the Matrix to another. Presumably, they tracked the call. – Harry Johnston Jun 21 '15 at 4:17
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    @HarryJohnston - The presumption is that the agents were on their way to Neo's office BEFORE Neo took the call. Plus, if the only reason the Agents came is because they tracked the call, then you're saying if they didn't make the call, the agents would not have come? That can't be right. The reason they called him was to warn him that the agents were already on their way. – Kevin Fegan Jun 23 '15 at 10:00
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You are taking Agent Smith's statement too literally. He doesn't mean that Morpheus personally contacted Neo, he means that Morpheus' crew (specifically Trinity) contacted Neo. He knows this because Cypher is a traitor.

Here's the first conversation of the movie:

Cypher: We're going to kill him, do you understand that?

Trinity: Morpheus believes he is the One.

Cypher: Do you?

Trinity: It doesn't matter what I believe.

Cypher: You don't, do you?

Trinity: Did you hear that?

Cypher: Hear what?

Trinity: Are you sure this line is clean?

Cypher: Yeah, of course I'm sure.

Trinity: I better go.

The Matrix (transcript)

Later, after Trinity has just escaped (because the line wasn't clean thanks to Cypher) the Agents have this conversation:

Agent Brown: She got out.

Agent Smith: It doesn't matter.

Agent Brown: The informant is real.

Agent Smith: Yes.

Agent Jones: We have the name of their next target.

Agent Brown: The name is Neo.

Agent Smith: We'll need a search running.

Agent Jones: It has already begun.

The Matrix (transcript)

The Agents therefore know that Cypher is a true informant, and they know from him that Neo is the "next target" of Morpheus' crew. Since Morpheus is the captain of that crew, Morpheus has indirectly contacted Neo. Moreover, Agent Smith is not talking about the phone call Morpheus personally made to Neo just prior to Neo's capture, he's talking about Neo's earlier contact with Morpheus' crew.

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I think it worth adding that this is the 6th version of the Matrix and that Neo and his abilities are known to and even designed by the machines. I don't know if Agent Smith knew that, but I think it is not out of the realm of possibility that the programs running the Matrix (such as the Architect) marked Neo out for Smith's surveillance. Even if there hadn't been a connection between Neo and Morpheus yet, it's plausible that the machines knew that there would be at some point between Neo and the resistance.

Additionally, since the fabric of the reality itself is written in computer code within the Matrix, I wouldn't rule out near-infinite surveillance and instantaneous travel (by taking over people's bodies??).

All that said, my (hazy) first impression of that scene was that they were coming to arrest him for hacking of some kind.

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