Corrected entry: Cypher alerts the agents to the location of Morpheus' base of operations via cell phone tracing. But since the agents can transport to any body in the Matrix that hasn't been unhooked, and they can trace calls in about 30 seconds as we saw at the start, it would have been easier if they had transported to the nearest bodies, got into the building, killed Mouse, destroyed their equipment and then summon the police. All this they could have done in 5 minutes while everyone was at the Oracle, but instead we get a very long, action packed confrontation.
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Correction: The agents made a different call, they wanted to trap the entire party but their primary target was Morpheus and they had to make sure he wouldn't get away. Anything else they tried could cause Morpheus to escape.
lionhead