For years, a clandestine U.S. intelligence team had tracked a man they knew was high in the leadership of al Qaeda — an operative some believed had a hand in plotting the gruesome 2009 suicide attack in Afghanistan that killed seven CIA officers. Their pursuit was personal, and by early 2014 the agency had the target under tight drone surveillance. “We literally had a bead on this guy’s head and just needed authorization from Washington to pull the trigger,” said the source. Then something unexpected happened. While agents waited for the green light, the al Qaeda operative’s name, as well...