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.

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 C.I.A.’s network of secret prisons, paved the way for the C.I.A. 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…

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

The report was the beginning of the end for the program. The prisons would stay open for several more years, and new detainees were occasionally picked up and taken to secret sites, but at Langley, senior C.I.A. officers began looking for an endgame to the prison program. One C.I.A. operative told Mr. Helgerson’s team that officers from the agency might one day wind up on a “wanted list” and be tried for war crimes in an international court.