At the NYPD, the FBI's concerns about the Shehadeh case are chalked up to the inevitable strains that sometimes occur in policing. NYPD officials promised to work more closely with the FBI, to share information earlier, federal and city officials said. FBI officials, too, promised to be more open about their cases. The goal was to make sure something like that didn't happen again.
In 2009, federal prosecutors in Boston charged Terak Mehanna in a terror plot. The Justice Department said he and his friends conspired to travel to Yemen for terrorism training so they could fight the U.S. in Iraq.
While Mehanna was in jail in Boston, a source working with the NYPD was in contact with Mehanna, according to current and former FBI and NYPD officials involved in the case. Such contact with another agency's suspect, who's already been charged, is considered improper.
The NYPD dispatched senior officials to Boston to explain to the Justice Department what happened, according to people briefed on the meeting. The NYPD said the contact with Mehanna was inadvertent, part of an unrelated investigation with clear New York ties.
The FBI asked, how could it be inadvertent when the NYPD was working 200 miles outside its jurisdiction?
In an interview last year, NYPD spokesman Paul Browne made a distinction between the NYPD "making contact" with Mehanna and "having contact" with him.
"We did not initiate any contact," Browne said.
He would not elaborate.
At trial, Mehanna's lawyers asked what the Justice Department knew about the NYPD's contact with Mehanna.
"We are not aware of any such contact," Assistant U.S. Attorney Aloke Chakravarty said.
Mehanna was convicted of terrorism charges in December and awaits sentencing. His lawyers said they still don't know how the NYPD was involved with their client.
As Cohen was expanding his department's counterterrorism mission, documents show that he also steered the NYPD into the murky world of counterintelligence.
Counterintelligence includes spying on other nation's spies inside the United States. Under a 1981 presidential order, that's supposed to be coordinated by the FBI. But as home to the United Nations, New York is a major arena for U.S. spy games.
In 2006, documents show, the NYPD focused on the Iranian threat, believing that Iran's government or its proxies, including the Hezbollah terrorist organization, might strike at New York City. It fanned out across the Northeast, looking for Shiite mosques and other places where Iranians might gather. The goals were to spot potential problems and develop informants with ties to Iran and Hezbollah.
In one highly unusual operation, the NYPD recruited a source close to the Iranian Mission at the United Nations, former senior NYPD officials said. Police had tried something similar before, former federal officials said, and crossed paths with the FBI. But this time, the FBI didn't know about it.
The Associated Press is withholding details of the operation for national security reasons.
Normally, agencies coordinate their efforts, a process known as deconfliction. Without it, two investigators might work the same source. One agency's informant might be the target of another agency's investigation. That can undermine cases and hurt both efforts.
Cohen's team recruited the source on its own, the former NYPD officials said.
The source gave the NYPD unique insight into the Iranian mission, a connection that the NYPD hoped would provide them early warning of Iranian collaborators in the city. But it also infringed on the turf of the FBI and the CIA, which have longstanding counterintelligence sources across the diplomatic terrain of New York City.
Cohen and Browne did not return several messages asking whether they had any comment or concerns about the AP reporting on this incident.
NYPD documents also show that police used one of its telephone pole-mounted video cameras to monitor the Saudi Mission, another sensitive diplomatic and counterintelligence location.
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