But after a decade of often inconclusive efforts against al-Qaeda, the Obama administration has relied on new levels of collaboration between the CIA and JSOC to push the terrorist network closer to collapse…

Even leadership ranks have begun to blur: Former CIA director Leon E. Panetta is now secretary of defense; David H. Petraeus, previously the military commander in Iraq and Afghanistan, is just weeks into his new assignment as head of the CIA.

The attack on Aulaqi blended capabilities from both sides, and was carried out under CIA authority that allowed for greater latitude in conducting lethal operations outside conventional war zones. The military aircraft came across the Gulf of Aden from Djibouti, which has been the primary base for JSOC drones patrolling Yemen for much of the past year.

U.S. officials said that CIA drones involved in the strike took off from an agency base in the Arabian peninsula so new that it had become operational only in recent weeks.