At the cutting edge of the U.S. military’s campaigns against al-Qaeda and its offshoots over the past 14 years has been an organization still unused to the spotlight. Born from the wreckage of the United States’s failed attempt to rescue its hostages in Iran in 1980, Joint Special Operations Command was created to provide a standing headquarters that could run similar operations in the future. But although JSOC (pronounced “jay-sock”) had grown significantly in its first two decades, on September 11, 2001, it remained a fringe presence on the U.S. military scene, with a narrowly circumscribed set of responsibilities that included short-term counterterrorist missions, operations to secure weapons of mass destruction, and very little else.

Since then, however, as the United States has grappled with an interconnected web of Islamist terror networks around the world, uniformed and civilian leaders have increasingly relied on one JSOC specialty in particular: its proficiency at the “manhunt,” the most famous recent example of which was the May 2011 raid that killed Osama bin Laden. But it is a skill the command has been honing, at some cost, for most of its history, and it is one that has become central to the current U.S. campaign against ISIS. In that sense, JSOC’s history says a great deal about America’s future in the Middle East.

By far the most ambitious operation of JSOC’s first decade—one that would foreshadow its future in the global war on terror—was its lead role in the U.S. invasion of Panama. Following years of escalating tensions between the United States and Panamanian dictator Manuel Noriega, culminating in Panamanian Defense Forces personnel killing a U.S. Marine, in mid-December 1989 President George Bush gave the order to depose Noriega. The dictator went to ground during the invasion’s first hours, and operators from the Army’s Delta Force and the Navy’s SEAL Team 6—the elite “special-mission units” at the core of JSOC—pursued him and his associates in what Carl Stiner, a former JSOC commander who led the invasion force, later described as “one of the most intensive manhunts in history.” Operators kicked in doors of safe house after safe house, immediately interrogated any Noriega cronies they found, and then launched new missions based on that intelligence.

These nonstop operations set a precedent for future missions in Afghanistan and especially Iraq. Although nobody in 1989 was talking about Noriega’s “network,” that’s exactly what JSOC was attacking. But the Noriega manhunt also taught the command how difficult it can be to find someone who is on his own turf and doesn’t want to be found. Noriega stayed one step ahead of the task force until December 24, when he took refuge in in the papal nunciature—the Vatican’s embassy in Panama—and was flown to the United States following his surrender on January 3, 1990. His signature red underwear, which he believed protected him from harm, ended up in a display case at Delta’s compound in Fort Bragg, North Carolina.

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When Iraq invaded Kuwait in August 1990, JSOC also did “a lot of planning” for the most sensitive mission possible: sending undercover operators into Baghdad to kill Iraqi dictator Saddam Hussein, according to a Pentagon special-operations source. “There was an effort to just solve the problem by taking out Saddam Hussein,” the source said. JSOC considered a range of methods, from shooting the dictator with small arms to having operators call in an air or missile strike. In the end, the officer said, the planning foundered on an all-too-common failing: “The intel just could not provide the proper foundations for being able to launch a mission like that.”

Indeed, in manhunting, actionable intelligence is the coin of the realm. Nowhere was that more apparent than in Colombia, where JSOC soon became actively engaged in another manhunt, for the drug lord Pablo Escobar. For more than a year beginning in 1992, JSOC rotated Delta and Team 6 operators through the country, keeping a force of about a dozen between Bogota, the capital, and Medellin, Escobar’s hometown. Their mission was supposed to be limited to training the “Search Bloc,” the Colombian force going after Escobar and his henchmen, but the American operators found ways to accompany their trainees on missions, while another unit worked to zero in on Escobar’s radio and cell-phone calls. Escobar knew he was being tracked, so he kept his conversations short and always operated in a way that aimed to mislead the searchers about his real location.

But on December 2, 1993, he finally made a mistake, staying on the phone with his son for several minutes instead of the customary 20 seconds. The phone-tracking devices the Americans had taught the Colombians to use led the Search Bloc straight to a two-story house. Escobar and his bodyguard were gunned down as they tried to flee across the rooftops. Persistent rumors suggested that the shot that killed the drug lord was made by a U.S. operator, perhaps a sniper stationed on a nearby rooftop. No one has ever produced any evidence or witness that validates this claim, and Jerry Boykin, who was then the Delta commander, has gone on record to say his men didn’t pull any triggers that day.

Whoever took the final shot, JSOC chalked Escobar’s death up as a successful mission. The mission would also have long-lasting impact on the command, as it provided the template for how to use a quarry’s cell phone to track him down. The mission also underlined a lesson learned four years earlier by operators who had hunted Noriega through Panama City: Finding a man of resources who is hiding in his hometown is a difficult task.

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As the search for Escobar was reaching its climax in the fall of 1993, another, much larger JSOC task force on the other side of the world was learning a similar lesson. That manhunt did not end quite as well. Mohammed Farah Aideed, a Somali warlord who controlled much of Mogadishu, the capital, was waging war on the United Nations-backed international peacekeeping force that had deployed to deliver humanitarian assistance to the famine-gripped East African nation. In August, U.S. President Bill Clinton approved the deployment of a JSOC task force to capture Aideed.

JSOC put the lessons learned in Panama and Colombia to use and launched half a dozen operations in August and September designed to strip away the layers of protection that surrounded Aideed. On the afternoon of October 3, based on an informant’s tip, the task force launched a seventh mission, an air-assault raid on a meeting of Aideed’s inner circle at the Olympic Hotel in the Bakara Market neighborhood, the very heart of Aideed territory. The timing of the raid was not ideal—JSOC preferred to operate at night rather than in broad daylight—but the transitory nature of the opportunity left the task force little choice.

The raid was going well until a militiaman shot down a Black Hawk helicopter with a rocket-propelled grenade. About 20 minutes later, another RPG downed a second Black Hawk. What had been a routine, if dangerous, mission that should have lasted no longer than an hour descended into chaos. The battle left 18 U.S. soldiers dead and scores wounded, as well as many hundreds of Somali casualties. Aideed remained at large.

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What became known as the “Black Hawk Down” incident showed that, while in theory targeting individuals was an economical and efficient way to wage war, in practice the costs could still be incredibly high. Yet following the terrorist attacks of September 11, 2001, the Defense Department made manhunting a priority. Throughout the first year after those attacks, the department’s most senior military and civilian officials were “trying to understand how do you defeat an organism or a network,” said a Joint Staff officer who was deeply involved. “First of all we said, ‘Hey, we can do it by [eliminating] leadership.’” He described the strategy as “cutting off the head of the snake.” That approach, so enticing to policymakers because it seemed to offer a neat solution to the intractable global problem of violent anti-Western Islamism, also perfectly matched JSOC’s skill set, something not lost on then-Defense Secretary Donald Rumsfeld.

On July 1, 2002, the defense secretary sent a memo to Undersecretary of Defense for Policy Douglas Feith, titled “Manhunts.” “How do we organize the Department of Defense for manhunts?” the memo asked. “We are obviously not well organized at the present time.” The memo reflected a critical moment for Rumsfeld and JSOC, according to Bob Andrews, then the acting assistant secretary of defense for special operations and low-intensity conflict. “Once he fastened on the manhunt thing, he looked at that as the silver bullet against terrorism,” he said. Dell Dailey, then the head of JSOC, sent an officer to Israel to speak to officials there about their experiences with manhunting, and in particular the years-long effort to track down and kill the Palestinian Black September terrorists who murdered 11 Israeli athletes at the 1972 Munich Olympics.

The next several years would prove that a so-called decapitation approach to counterterrorism was no silver bullet, but in the spring and summer of 2002 its limitations were far from clear. The formula was known as “two-plus-seven,” but in reality it quickly expanded to “two-plus-seven-plus-30,” best envisioned as a series of concentric circles with Osama bin Laden and his deputy Ayman al-Zawahiri in the bull’s eye. The ring around them consisted of seven key al-Qaeda facilitators, surrounded by an outer ring of 30 slightly less senior but still important al-Qaeda operatives. As one of the seven was captured or killed, the next in line from the outer 30 would take his place in the diagram. “Eventually, I think essentially almost all of them are captured or killed,” said the Joint Staff officer. “And so they change out.”

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The war in Iraq gave the command a laboratory in which to perfect its manhunting techniques. After the fall of Baghdad, JSOC’s first task was to pursue dozens of senior figures from Saddam Hussein’s regime who were on the run. After finding and killing Saddam’s sons Uday and Qusay in July 2003, JSOC brought that phase of the war to an end on December 13 when operators captured Saddam Hussein in a hole outside his hometown of Tikrit.

But by then it was becoming clear that the Hussein-era figures were yesterday’s men. The struggle in which the United States was embroiled in Iraq was complex, combining traditional insurgency, Islamist terrorism, sectarian civil war, tribal conflict, and a proxy war with Iran. On June 29, 2005, JSOC’s commander, Stanley McChrystal, received a summons to the White House to brief a National Security Council session on Abu Musab al-Zarqawi, the leader of the insurgent group al-Qaeda in Iraq. When McChrystal concluded, Bush asked him: “Are you going to get him?” “We will, Mr. President,” McChrystal replied. “There is no doubt in my mind.”

As that meeting indicated, despite the complexity of the fight in Iraq, the administration increasingly saw the war as a struggle with one man’s organization. To a degree, this reflected the thinking among the military leaders in Baghdad, who over the course of a few months had grown convinced that removing Zarqawi from the battlefield would collapse the insurgency. McChrystal’s task force in Iraq was locked in a deadly contest with the leader of al-Qaeda in Iraq, as operators and intelligence analysts raced to devour the middle ranks of his network before he could replenish them. Zarqawi, meanwhile, was trying to ignite a full-scale sectarian civil war before the task force destroyed his organization, which he had presciently designed to function as semi-autonomous regional and local cells. On February 22, 2006, explosives planted by his fighters destroyed the golden dome of the Al-Askari mosque in Samarra, one of Shiite Islam’s most sacred places. The bombing initiated an intense cycle of Sunni versus Shiite violence.

By that spring, the task force’s hunt for Zarqawi had become a higher JSOC priority than its search for bin Laden and Zawahiri. “Who’s the biggest threat right now?” said a special operations source at the time. “In military terms, bin Laden has been neutralized. He’s not going anywhere. He can’t really move. His communications are shallow. ... Zarqawi is a bigger threat.” By late May, the task force had managed, through interrogating captured al-Qaeda in Iraq operatives, to map out the group’s command structure around Baghdad, and they identified a man named Abd al-Rahman as Zarqawi’s spiritual advisor. For three weeks, the task force monitored Rahman in the hope that he’d lead them to Zarqawi.

He did.

On June 7, a drone tracked Rahman as he was driven north out of Baghdad, following him to a two-story house in Hibhib, a village only a dozen miles from McChrystal’s headquarters in Balad. Analysts, operators, and staffers on the ground watched in rapt attention as a stout man in black walked out and took a late afternoon stroll down the driveway before returning to the house. It had to be Zarqawi. At 6:12 p.m., an F-16 dropped a laser-guided 500-pound bomb on the house and followed it less than two minutes later with another bomb. The house disintegrated. A cheer erupted in the Balad operations center. Eighteen minutes later, Delta operators arrived to find Iraqi police loading Zarqawi on a gurney—still alive, but suffering from severe internal blast injuries. He died in front of them.

Bush called McChrystal that night to congratulate him. But any hopes that Zarqawi’s death would signal an immediate downturn in the violence went unfulfilled. Al-Qaeda in Iraq quickly promoted Abu Ayyub al-Masri, the Egyptian who had been Zarqawi’s deputy, to replace his late boss, and the civilian death tolls kept climbing. (Al-Masri would go on to found the Islamic State of Iraq, which morphed into the Islamic State of Iraq and Syria after al-Masri himself was killed in a JSOC raid.) McChrystal’s assessment was blunt: “We had killed Zarqawi too late.”

In the years that followed, JSOC would achieve what for the command was an uncomfortable level of public recognition for running Operation Neptune Spear, the mission that killed Osama bin Laden in Abbottabad, Pakistan. But it was the manhunting campaign against al-Qaeda in Iraq that showcased JSOC’s effectiveness while also demonstrating the limits of an approach that relied so heavily on special-operations forces as the military’s main effort. Although JSOC seemed to have eviscerated al-Qaeda in Iraq by the time the United States pulled out of Iraq at the end of 2011, it had not completely destroyed it. Over the next three years, al-Qaeda in Iraq evolved into the Islamic State, which, after establishing a safe haven in war-torn Syria, swept across northern Iraq in 2014, seizing town after town from which JSOC and other U.S. forces had evicted al-Qaeda in Iraq at great cost several years earlier.

By 2015, JSOC was back in Iraq, operating from a base in Kurdistan and using signals and human intelligence to locate Islamic State leaders. The manhunt was on again.


This article has been adapted from Sean Naylor's forthcoming book, Relentless Strike: The Secret History of Joint Special Operations Command.