Brennan made frequent visits to Yemen and Saudi Arabia, its closest neighbor and the dominant regional power. He used his longtime contacts in the region to cement a joint U.S.-Saudi policy that would ultimately — with the help of Yemen’s Arab Spring revolt — bring a more cooperative government to power. He often spoke of the need to address “upstream” problems of poverty and poor governance that led to “downstream” radicalization, and pushed for economic aid to buttress a growing military and intelligence presence.

Yemen quickly became the place where the United States would “get ahead of the curve” on terrorism that had become so difficult to round in Pakistan, one official said. As intelligence and military training programs were expanded, the military attacked AQAP targets in Yemen and neighboring Somalia using both fixed-wing aircraft and drones launched from a base in Djibouti on the Horn of Africa.

Despite Brennan’s professed dismay at the transformation of the CIA into a paramilitary entity with killing authority, the agency was authorized to operate its own armed aircraft out of a new base in the Arabian Peninsula.

An opaque process

Where Obama and Brennan envision a standardized counterterrorism program bound by domestic and international law, some others see a secretive killing machine of questionable legality and limitless expansion.

Many civil libertarians and human rights experts disdain claims by Brennan and others that the drone program has become increasingly transparent, noting that the administration has yet to provide even minimal details about targeting decisions or to take responsibility for the vast majority of attacks.

“For more than two years, senior officials have been making claims about the program both on the record and off. They’ve claimed that the program is effective, lawful and closely supervised,” Jameel Jaffer, deputy legal director of the American Civil Liberties Union, said last month in appealing repeated court refusals to force the administration to release more information.

Some critics have described it as immoral, rejecting the administration’s claims that few civilians have been among the nearly 3,000 people estimated to have been killed in drone attacks. There is ample evidence in Pakistan that the more than 300 strikes launched under Obama have helped turn the vast majority of the population vehemently against the United States.

None of the United States’ chief allies has publicly supported the targeted killings; many of them privately question the administration’s claim that it comports with international law and worry about the precedent it sets for others who inevitably will acquire the same technology.

To the extent that it aspires to make the program’s standards and processes more visible, the playbook has been a source of friction inside the administration. “Other than the State Department, there are not a lot of advocates for transparency,” one official said. Some officials expressed concern that the playbook has become a “default” option for counterterrorism.