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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 Central Intelligence Agency (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 US, was a turning point for the CIA and provides a new context for the continuing debate nearly nine years later over President Barack Obama’s approach to fighting terrorism.

The attack in 2004, coming just a month after a blistering internal report about abuses in the CIA’s network of secret prisons, changed the focus of the war against al-Qaida from capturing terrorists to killing them, accelerating the transformation of an agency that began as a Cold War espionage service into a paramilitary organization.

The strike paved the way for hundreds of covert CIA drone attacks that have killed thousands of people, Pakistanis and Arabs, militants and civilians alike. Pakistan—more than any other country—has been 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 US as a nation goes to war.

Neither American nor Pakistani officials have ever publicly acknowledged what really happened to Muhammad—details of the attack, 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 O. 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 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."

©2013/The New York Times

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