The attitudes behind Obama’s drone policy have their roots in the Eisenhower era. Illustration by Noma Bar

In the summer of 1960, Sidney Gottlieb, a C.I.A. chemist, flew to Congo with a carry-on bag containing vials of poison and a hypodermic syringe. It was an era of relative subtlety among C.I.A. assassins. The toxins were intended for the food, drink, or toothpaste of Patrice Lumumba, Congo’s Prime Minister, who, in the judgment of the Eisenhower Administration, had gone soft on Communism. Upon his arrival, as Tim Weiner recounts in his history of the C.I.A., Gottlieb handed his kit to Larry Devlin, the senior C.I.A. officer in Léopoldville. Devlin asked who had ordered the hit. “The President,” Gottlieb assured him. In later testimony, Devlin said that he felt ashamed of the command. He buried the poisons in a riverbank, but helped find an indirect way to eliminate Lumumba, by bankrolling and arming political enemies. The following January, Lumumba was executed by the Belgian military.

For Eisenhower, who had witnessed the carnage of the Normandy landings and the Battle of the Bulge, and later claimed to “hate war as only a soldier who has lived it can,” political assassinations represented an alluring alternative to conventional military action. Through the execution or overthrow of undesirable foreign leaders, the thinking went, it might be possible to orchestrate the global struggle against Communism from a distance, and avoid the misery—and the risks of nuclear war—that out-and-out combat would bring. Assassination was seen not only as precise and efficient but also as ultimately humane. Putting such theory into practice was the role of the C.I.A., and the agency’s tally of toppled leftists, nationalists, or otherwise unreliable leaders is well known, from Mohammad Mosadegh, of Iran, in 1953, and Jacobo Árbenz Guzmán, of Guatemala, in 1954, to Ngo Dinh Diem, of South Vietnam, in 1963, and Salvador Allende, of Chile, in 1973. Not all the schemes went according to plan; a few seemed inspired by Wile E. Coyote. The C.I.A. once planned to bump off Fidel Castro by passing him an exploding cigar.

Aside from the moral ugliness of violent covert action, its record as a national-security strategy isn’t encouraging. On occasion, interventions have delivered short-term advantages to Washington, but in the long run they have usually sown deeper troubles. Lumumba’s successor, the dictator Joseph Mobutu, may have been an ally of the United States until his death, in 1997, but his brutal rule prepared the way for Congo’s recent descent into chaos. Memory of the C.I.A.’s hand in Mosadegh’s overthrow stoked the anti-American fury of the Iranian Revolution, which confounds the United States to this day. Foreign policy is not a game of Risk. Great nations achieve lasting influence and security not by bloody gambits but through economic growth, scientific innovation, military deterrence, and the power of ideas.

During the nineteen-seventies, it seemed as though this era of covert action were coming to an end. After a congressional investigation exposed the extent of C.I.A. plots, President Gerald Ford issued an executive order banning political assassinations. Successive Presidents strengthened the ban with executive orders of their own, codifying a growing bipartisan consensus that assassinations undercut America’s avowed commitment to democracy, human rights, and the rule of law.

But after September 11, 2001, as lower Manhattan and the Pentagon smoldered, C.I.A. leaders advocated for the right to kill members of Al Qaeda anywhere in the world. George W. Bush eagerly assented. On September 17th, the President signed a still classified directive delegating lethal authority to the agency. “The gloves come off,” J. Cofer Black, the director of the agency’s Counterterrorist Center, told Congress early in 2002.

Since then, America’s targeted-killing program has grown into a campaign without borders, in which the White House, the C.I.A., and the Pentagon all play a part. The role of armed drones in this war is well known, but for years neither President Obama nor his advisers officially acknowledged their existence. Some three thousand people, including an unknown number of civilians, are believed to have died in targeted strikes since 2001. If the death tolls from strikes in Iraq and Afghanistan were included, the figure would be much higher.

An assassination campaign against suspected terrorists is not the same as one that occasionally rubs out unfriendly political leaders of nation-states, but it raises similar questions. Is a program of targeted killing, conducted without judicial oversight or public scrutiny, consistent with American interests and values?

The return of Presidentially sanctioned assassinations is described in two new books of investigative journalism, “The Way of the Knife” (Penguin), by Mark Mazzetti, a Times reporter; and “Dirty Wars” (Nation), by Jeremy Scahill, of The Nation. In the wake of September 11th, the C.I.A. launched what now seems a comparatively selective effort to capture or kill “high-value targets” associated with Al Qaeda. President Bush kept a list of two dozen senior terrorists in the Oval Office and reportedly crossed out their photographs when they were eliminated or imprisoned.

The Iraq War lifted targeted killing to an industrial scale. Frustrated by the lead role taken by the C.I.A., Defense Secretary Donald Rumsfeld urged the Pentagon’s clandestine forces, under the Joint Special Operations Command, to add terrorist hunting to their specialties. As one insurgent group after another sprang up to resist the American occupation of Iraq, JSOC was given an opportunity to prove itself.

Between 2003 and 2008, Special Operations forces in Iraq, under the leadership of General Stanley McChrystal, perfected a system of intelligence collection, detention, and targeted killing. In blistering night raids, McChrystal’s men would descend upon the homes of suspected insurgents, kill or capture them, and then comb their phones and e-mails for intelligence, which was used to identify fresh targets for attack. This program has been described by other journalists, and aspects of it were depicted in the film “Zero Dark Thirty.” Scahill adds a thorough and unsentimental accounting of JSOC’s brutal work in Iraq, including a review of the available evidence that prisoners interrogated at its facilities near Baghdad were tortured.

As the sharp end of a counter-insurgency strategy, McChrystal’s approach resembled the C.I.A.’s Phoenix program during the Vietnam War, when the United States tried, and failed, to suppress the Vietcong by detaining and assassinating thousands of suspected militants and cadre leaders. Yet the tactics and assumptions that McChrystal developed were not confined to Iraq’s declared battlefield. Increasingly, the C.I.A. and JSOC came to see their campaign against Al Qaeda as a worldwide counter-insurgency. They believed, as Scahill’s subtitle aptly suggests, that “the world is a battlefield.” Before long, they had constructed a Phoenix program with global reach.

After 2006, as the Taliban regrouped, McChrystal brought his system of intelligence collection and targeted killing to bear in Afghanistan. Although the Taliban’s top leaders were hiding out in Pakistani cities such as Quetta and Karachi, McChrystal was able to launch successful strikes against mid-level commanders. Then, in 2009, President Obama ordered tens of thousands of additional troops to Afghanistan, and asked McChrystal to command all American and international forces. The appointment was a signal to the C.I.A. and the Pentagon that assassination would be a critical, if often undeclared, element in the effort to suppress the Taliban.

The influx of international forces inflamed Taliban fighters, who had important bases in the tribal border areas of Pakistan. At the urging of his advisers, Obama escalated clandestine drone strikes inside Pakistan in an attempt to disrupt these safe havens. President Bush, worried about destabilizing the country’s already weak government, had avoided this escalation until very late in his Presidency. Bush oversaw forty-eight drone strikes in Pakistan during his two terms. Since 2009, Obama has authorized more than three hundred. In Mazzetti’s telling, C.I.A. leaders repeatedly pushed Obama for more expansive authority to use armed drones. They got their way in almost every instance.