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 Mr. 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.
Mr. Muhammad and his followers had been killed by the C.I.A., 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 C.I.A. 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.
The C.I.A. 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.By 2004, Mr. Muhammad had become the undisputed star of the tribal areas, the fierce mountain lands populated by the Wazirs, Mehsuds and other Pashtun tribes who for decades had lived independent of the writ of the central government in Islamabad. A brash member of the Wazir tribe, Mr. Muhammad had raised an army to fight government troops and had forced the government into negotiations. He saw no cause for loyalty to the Directorate of Inter-Services Intelligence, the Pakistani military spy service that had given an earlier generation of Pashtuns support during the war against the Soviets.

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