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FILE - This Sunday, Jan. 31, 2010 file photo shows a U.S. Predator drone as it flies over the moon above Kandahar Air Field, southern Afghanistan. A U.S. drone fired a pair of missiles that hit a vehicle in northwestern Pakistan, near the Afghan border killing three suspected militants, in Datta Khel village of North Waziristan tribal region at about midnight Thursday, two intelligence officials said.

Kirsty Wigglesworth, Associated Press - Ap

Residents from Pakistani tribal areas hold a protest with supporters of Pakistani religious party to condemn US drone attacks on militants' hideouts in tribal areas , in Peshawar, Pakistan, Monday, March 4, 2013. Dozens of people demanded to halt drone attacks which reportedly killed many civilians. Banner at right reads, "what wrong did I do to America," and left, "this is home not the headquarters of terrorists."

Mohammad Sajjad, Associated Press - Ap

How the CIA made a deal with Pakistan to open door to targeted killings

  • Article by: MARK MAZZETTI
  • New York Times
  • April 6, 2013 - 10:12 PM

Nek Muhammad knew he was being followed.

On a hot day in June 2004, the Pashtun tribesman was lounging inside a mud compound in South Waziristan, speaking by satellite phone to one of the many reporters who regularly interviewed him on how he had fought and humbled Pakistan’s army in the country’s western mountains. He asked one of his followers about the strange, metallic bird hovering above him.

Less than 24 hours later, a missile tore through the compound, severing Muhammad’s left leg and killing him and several others, including two boys, ages 10 and 16. A Pakistani military spokesman was quick to claim responsibility for the attack, saying that Pakistani forces had fired at the compound. That was a lie.

Muhammad and his followers had been killed by the CIA, the first time it had deployed a Predator drone in Pakistan to carry out a “targeted killing.” The target was not a top operative of Al-Qaida, but a Pakistani ally of the Taliban who led a tribal rebellion and was marked by Pakistan as an enemy of the state. In a secret deal, the CIA had agreed to kill him in exchange for access to airspace it had long sought so it could use drones to hunt down its own enemies.

That back-room bargain, described in detail for the first time in interviews with more than a dozen officials in Pakistan and the United States, is critical to understanding the origins of a covert drone war that began under the Bush administration, was embraced and expanded by President Obama, and is now the subject of fierce debate. The deal, a month after a blistering internal report about abuses in the CIA’s network of secret prisons, paved the way for the CIA to change its focus from capturing terrorists to killing them, and helped transform an agency that began as a Cold War espionage service into a paramilitary organization.

The CIA since has conducted hundreds of drone strikes in Pakistan that have killed thousands of people, Pakistanis and Arabs, militants and civilians alike. While it was not the first country where the United States used drones, it became the laboratory for the targeted killing operations that have come to define a new American way of fighting, blurring the line between soldiers and spies and short-circuiting the normal mechanisms by which the United States as a nation goes to war.

Neither American nor Pakistani officials have ever publicly acknowledged what really happened to Muhammad — details of the strike that killed him, along with those of other secret strikes, are still hidden in classified government databases. But in recent months, calls for transparency from members of Congress and critics on both the right and left have put pressure on Obama and his new CIA director, John Brennan, to offer a fuller explanation of the goals and operation of the drone program, and of the agency’s role.

Brennan, who began his career at the CIA and over the past four years oversaw an escalation of drone strikes from his office at the White House, has signaled that he hopes to return the agency to its traditional role of intelligence collection and analysis. But with a generation of CIA officers now fully engaged in a new mission, it is an effort that could take years.

Today, even some of the people who were present at the creation of the drone program think the agency should have long given up targeted killings.

Ross Newland, who was a senior official at the CIA’s headquarters in Langley, Va., when the agency was given the authority to kill Al-Qaida operatives, says he thinks that the agency had grown too comfortable with remote-control killing, and that drones have turned the CIA into the villain in countries like Pakistan, where it should be nurturing relationships in order to gather intelligence. As he puts it, “This is just not an intelligence mission.”

As the drone negotiations were taking place, the CIA’s inspector general, John Helgerson, had just finished a searing report about the abuse of detainees in the CIA’s secret prisons. The report kicked out the foundation upon which the CIA detention and interrogation program had rested. It was perhaps the single most important reason for the CIA’s shift from capturing to killing terrorism suspects.

The ground had shifted, and counterterrorism officials began to rethink the strategy for the secret war. Armed drones, and targeted killings in general, offered a new direction. Killing by remote control was the antithesis of the dirty, intimate work of interrogation. Targeted killings were cheered by Republicans and Democrats alike. Before long the CIA would go from being the long-term jailer of the United States’ enemies to a military organization that erased them.

© 2014 Star Tribune