“Sir, big A.Q. operators. We’ve been trying to track them forever. They’re really careful. They’ve been hard to find. They’re the first team.”

Another pause. A long one.

“Use the GBU. And that small building they sometimes use as a dorm …”

“Yes, sir.”

“After the GBU hits, if military-age males come out …”

“Yes, sir?”

“Kill them.”

Less than an hour later he is briefed again. The two targets are dead. The civilians have fled the compound. All are alive.

TARGETED killing using drones has become part of the American way of war. To do it legally and effectively requires detailed and accurate intelligence. It also requires some excruciatingly difficult decisions. The dialogue above, representative of many such missions, shows how hard the commanders and analysts work to get it right.

The longer they have gone on, however, the more controversial drone strikes have become. Critics assert that a high percentage of the people killed in drone strikes are civilians — a claim totally at odds with the intelligence I have reviewed — and that the strikes have turned the Muslim world against the United States, fueling terrorist recruitment. Political elites have joined in, complaining that intelligence agencies have gone too far — until they have felt in danger, when they have complained that the agencies did not go far enough.

The program is not perfect. No military program is. But here is the bottom line: It works. I think it fair to say that the targeted killing program has been the most precise and effective application of firepower in the history of armed conflict. It disrupted terrorist plots and reduced the original Qaeda organization along the Afghanistan-Pakistan border to a shell of its former self. And that was well before Osama bin Laden was killed in 2011.

Not many years before, the targeted killings were fairly limited. But by 2008, we knew that the terrorist threat had increased to intolerable levels, both to American forces in South Asia and to the United States itself. From our surveillance platforms, we could observe training camps where men leapt off motorbikes and fired on simulated targets. Early that year, the C.I.A. and I began recommending more aggressive action.