NEW YORK — 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 Qaeda, 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 has since 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.
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 give up targeted killings because they have turned the CIA into a villian in countries where it is trying to gather information.