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At the beginning of the first Matrix film, Agents track down Trinity at the derelict Heart O' The City Hotel, aided by the fact that Trinity had been conversing on a line that wasn't "clean" in spite of Cypher's assurances to the contrary. Although the Agents fail to capture Trinity, they conclude that

"The informant is real."

The choice of words clearly indicates that they did not know if an informant really existed, let alone the specific identity of the traitor in Morpheus' ranks.

How did they know prior to Trinity's Heart O' the City incident that Morpheus, or another Zion captain, may have had a traitor in his/her ranks? What made the Agents think that an informant willing to work with them may exist? Was it because Cypher initiated contact prior to the Heart O' The City incident and, if so, how did he do so without revealing his identity?

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    I don't think it's a question of whether he existed, but rather, whether he was actually giving them reliable information or not. Once they confirmed that his first tip was real, they decided he wasn't a double agent. – Chris Hayes May 22 '15 at 22:13
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It's pretty clear that before the start of the film Cypher had already made contact with the agents, presumably by telephone and passed them information about the whereabouts of Morpheus and his crew.

The agents (only semi-believing him) are commenting on the fact that his information seems to be valid and that he personally does exist rather than the whole thing being merely a ruse constructed by the Zionese rebels for some odd purpose of their own.

This is more baldly stated in an earlier version of the script dated from 1997:

His jaw sets as he grinds his molars in frustration. AGENT JONES walks up behind him.

AGENT JONES: Then the informant is real.

AGENT SMITH: Does that surprise you? It was inevitable.

AGENT JONES: He'll be contacting us again.

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