Yet of all the government agencies likely to benefit, in terms of money and power, under the new administration, the winner may well be the CIA. Not the CIA’s leaders in Washington, to be sure. The incoming president seems eager to cut some of the agency’s senior spies and analysts. Instead, power would flow to operatives in the field — those who help arm allied foreign military forces, manage drone strikes, command small battles and reportedly kill enemy fighters in places from Somalia to Syria to West Africa to Afghanistan.

Incoming national security adviser Michael Flynn has suggested as much. It’s also the most politically expedient way to conduct the war on terrorism at a time when there is little public appetite for conventional military intervention. And so the Trump administration is poised to accelerate a transformation that has been happening, in fits and starts, since the 1960s, with the CIA becoming less of an outfit focused on spying and more of a paramilitary organization with a central role in violent conflicts.

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Further increasing the use of CIA paramilitaries and the Pentagon’s Special Forces in places such as Syria and Afghanistan would have potentially grave consequences for U.S. foreign policy — and for the United States’ leadership in the world. These paramilitaries are almost totally unaccountable, and unaccountability encourages rash, even criminal, behavior, including disdain for civilian lives, torture and other abuses. And, as demonstrated by a secret war in the 1960s and early ’70s — the most important precedent for today’s war on terror — it’s hard to win by using the CIA and Special Forces rather than conventional troops.

Fifty-six years ago, another incoming president decided to empower the CIA’s paramilitaries, relying on covert war rather than conventional fighting.

Before taking the oath of office in 1961, John F. Kennedy had (privately) squabbled with some CIA leaders, who saw him as inexperienced and potentially reckless.

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The CIA was only 14 years old then and a relatively small player in the American policymaking apparatus, one with far less power and fewer resources than the Departments of Defense and State. The agency mostly concentrated on traditional intelligence and political work, such as spying and trying to overthrow foreign governments believed unfriendly to the United States. It did a small amount of training of foreign forces, but no battlefield commanding.

Once in office, however, Kennedy approved the expansion of what would become the largest covert U.S. operation in history, in the tiny Southeast Asian nation of Laos. In a shift that could prove familiar in 2017, his decision dramatically empowered the same CIA that had worried about the new president.

The political climate at the time Kennedy took office also was in some ways similar to today’s. After a bloody stalemate in Korea, and the defeat of U.S.-backed French troops in Vietnam in 1954, many Americans were tired of conventional war and interventionism in general. Yet foreign policy elites believed that the United States faced an existential threat: Communism was spreading through Asia, first to China and North Vietnam and then to Laos, and possibly beyond. A secret war, one that used relatively few U.S. combatants and relied on foreign proxy forces and bombing from above, came to be seen as the safest choice, politically, for the Kennedy administration.

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The CIA’s involvement in Laos, which expanded in 1961 with a small training program for anti-communist fighters, ramped up quickly. It would grow over the course of the 1960s and into the early 1970s, with few Americans, and not even many members of Congress, knowing anything about it. The CIA recruited tens of thousands of U.S. contractors, paramilitary fighters and local Laotian warriors in an ultimately futile attempt to transform Laotian guerillas into a conventional army capable of stopping Hanoi and its local allies. U.S. bombers, working in concert with CIA paramilitaries, destroyed much of Laos while attacking Laotian and North Vietnamese communists. They dropped more bombs on Laos than on Germany and Japan combined in World War II. The country was left with so much unexploded ordnance that, in the four decades since Laos’s civil war ended in 1975, the leftover bombs have killed 20,000 Laotians.

The war cemented the CIA’s place as an organization with power on par with the Departments of Defense and State — and one increasingly dedicated to activities such as arming and advising foreign forces, managing conflicts and even overseeing targeted killings. CIA operatives went on to play roles in covert wars in Central America and Afghanistan in the 1980s, as well as in conflict zones in the war on terror. As Foreign Policy magazine has characterized it, the CIA is now “pulling the strings of U.S. foreign policy” — overseeing drone strikes and managing many aspects of the fight against the Islamic State. And according to documents released by former National Security Agency contractor Edward Snowden, the CIA’s budget appears to be greater than the State Department’s, a dramatic reversal from the early Cold War. While Brennan is recognized for leading an effort to reduce walls between operatives and analysts and fortify some of the agency’s traditional functions, he also oversaw an increase in the strength of paramilitary operations. In 2015, he promoted a paramilitary operative to head the clandestine branch — reportedly the first time a paramilitary officer took on the top undercover position.

Although Trump’s rhetoric suggests that he could rein in the CIA, the reality, as during Kennedy’s time, will probably be the reverse. The agency’s paramilitary branch, along with the military’s Special Forces — the two have become intertwined in policy and practice — will be further unleashed in a twilight war.

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Flynn is among those pushing such a strategy. A retired Army lieutenant general and former military intelligence officer, Flynn received a lot of media coverage for his conflicts with other intelligence leaders when he was the director of the Defense Intelligence Agency. But he has long argued that intelligence operatives should join U.S. Special Forces as central actors in what he sees as a “world war ” pitting the United States and Western democracies against Islamist militants. Flynn has been critical of the CIA’s analysts and called the organization overly political, but he also wants the United States to step up the pace of targeted actions against militants, presumably using Special Forces and CIA paramilitaries in a greatly expanded secret war. He has repeatedly praised the wisdom of CIA and Special Forces operatives closer to ground level. In a paper titled “Fixing Intel” that he wrote in 2010, he noted, “The soldier… on the ground is usually the person best informed about the environment and the enemy. Moving up through levels of hierarchy is normally a journey into greater degrees of cluelessness.”

Trump’s pick for CIA director, Rep. Mike Pompeo (R-Kan.), has similarly talked about Islamist terrorism as “the threat of our times.” And he has called for the United States to be more aggressive in the war on terror, but without using “100,000 soldiers to fight, U.S. soldiers, to fight in the Middle East, something I would not advocate for.”

Bolstering the CIA and Special Forces’ power fits the national zeitgeist, a combination of growing isolationism and fear of militant Islamist groups — a mix in some ways similar to the Cold War-era fear of communism. The Special Forces and the CIA’s paramilitary branch contain far fewer warriors than the conventional U.S. forces. Killed-in-action figures among the paramilitaries and Special Forces are usually much smaller than in a conventional war, so using them would be far less risky, politically, for the Trump administration.

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But in the long run, the increased use of CIA paramilitary operatives and Special Forces will prove counterproductive to U.S. values and goals.

Members of Congress receive limited information about how operations, including drone strikes and targeted killings, are conducted by the agency and Special Forces. According to reports in the New York Times, a small group of congressional staffers regularly travels to CIA headquarters to secretly witness the results of drone strikes, but does little else to investigate the specifics of the drone program or other CIA and Special Forces operations. Journalists, meanwhile, are rarely able to question CIA paramilitary operatives or leaders of the agency’s paramilitary branch, let alone travel with CIA and Special Forces units in the field. In contrast, journalists are given more on-the-ground access to operations involving conventional forces in places like Iraq and Afghanistan.

This lack of oversight increases the chances of field operatives using brutal, illegal tactics and getting away with it. One senior CIA paramilitary operative in Laos, Tony Poe, eventually wound up overseeing a band of tribal fighters loyal primarily to him, and — according to his own reports — supervising the killing of people linked to communist forces and occasionally dropping their heads from helicopters or mailing their severed ears back to the U.S. Embassy in Laos’s capital. He retired with accolades from the CIA.

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More recently, CIA operatives were responsible for overseeing black sites where alleged terrorists were detained and reportedly tortured under the George W. Bush administration. In a lengthy article this month, the Intercept documented allegations that individuals in SEAL Team 6, probably the most elite unit in the Special Forces or the CIA’s paramilitary branch, mutilated corpses, killed unarmed combatants and committed other abuses during operations in Afghanistan and Pakistan. Many of these actions reportedly took place more than a decade ago and never resulted in any real sanctions.

Secret wars also make victory hard to achieve. In Laos, as the CIA pushed its proxy army to fight bigger battles, backed by bombers, it bled local troops and soured many Laotian civilians on the U.S. presence. Having kept most advisers from U.S. conventional forces out of the operation, the CIA was unprepared for how to handle a growing war, with more conventional battles, and a public backlash in Asia.

Indeed, the Laos operation did not prevent a communist takeover there. It left U.S. allies devastated, with tens of thousands of refugees fleeing the country after the communists’ victory in 1975. When the war ended, one-tenth of Laos’s population had been killed or wounded, and more than 700 Americans had died, although these U.S. casualties were not fully acknowledged by Washington for decades.

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Turning a global conflict over to secret warriors poses the same risks today. The fighting could foster abuses with almost no oversight, kill civilians and thus alienate local populations. And secret forces simply may not have the ability to manage a widening conflict. If the new administration plans to really expand the field of fight, it will ultimately have to make more use of the conventional U.S. military.

Joshua Kurlantzick is senior fellow for Southeast Asia at the Council on Foreign Relations and the author of “A Great Place to Have a War: America in Laos and the Birth of a Military CIA,” from which this essay is adapted.

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