For every cloud of smoke that follows a CIA drone strike in Pakistan, dozens of smaller plumes can be traced to a gaunt figure standing in a courtyard near the center of the agency’s Langley campus in Virginia.

The man with the nicotine habit is in his late 50s, with stubble on his face and the dark-suited wardrobe of an undertaker. As chief of the CIA’s Counterterrorism Center for the past six years, he has functioned in a funereal capacity for al-Qaeda.