CHAPTER ELEVEN

Dark Matter

Besides the damage inflicted on the enemy by the CIA’s killer drones, paramilitary forces killed dozens of al-Qaeda leaders and hundreds of its foot soldiers in the decade after 9/11. But troops from a more mysterious organization, based in North Carolina, have killed easily ten times as many al-Qaeda, and hundreds of Iraqi insurgents as well.

This secretive organization, created in 1980 but completely reinvented in 2003, flies ten times more drones than the CIA. Some are armed with Hellfire missiles; most carry video cameras, sensors, and signals intercept equipment. When the CIA’s paramilitary Special Activities Division1 needs help, or when the president decides to send agency operatives on a covert mission into a foreign country, it often borrows troops from this same organization, temporarily deputizing them when necessary in order to get the missions done.

The CIA has captured, imprisoned, and interrogated close to a hundred terrorists in secret prisons around the world. Troops from this other secret military unit have captured and interrogated ten times as many. They hold them in prisons in Iraq and Afghanistan that they alone control and, for at least three years after 9/11, they sometimes ignored U.S. military rules for interrogation and used almost whatever means they thought might be most effective.

Of all the top secret units fighting terrorism after 9/11, this is the single organization that has killed and captured more al-Qaeda members around the world and destroyed more of their training camps and safe houses than the rest of the U.S. government forces combined. And although it greatly benefited from the technology produced by Top Secret America, the secret to its success has been otherwise escaping the behemoth created in response to the 9/11 attacks.

Over a decade in which they were fighting secret battles, sometimes in countries where wars have not been declared, this group of men (and a few women) sustained a level of obscurity that not even the CIA has managed to pull off. Its commanders—headquartered at Fort Bragg and the adjoining Pope Air Force Base in Fayetteville, North Carolina—still consider the organization to be officially “unacknowledged,” meaning its true purpose and everything it does is classified, and therefore, as far as the public is concerned, it does not exist.

“We’re the dark matter,” a strapping U.S. Navy SEAL once explained. “We’re the force that orders the universe but can’t be seen.”

When its officers are working in civilian government agencies or U.S. embassies abroad, which they do quite a lot, they dispense with uniforms, unlike the rest of their military comrades. On the battlefield, they dress according to the mission, and when in uniform they wear no name or rank identifiers. After 9/11, they had come up with all sorts of new names to hide their secret military subunits: The Secret Army of Northern Virginia, Task Force Green, Task Force Blue, Task Force 11, then Task Force 20, then Task Force 121. In fact, they change their task force numbers so often that even their American colleagues sometimes “aren’t sure who we are,” one officer explained, acknowledging that obscurity was the goal.

All these task forces are part of JSOC, which sits at the center of the secret universe as the dark matter that shapes the world in ways that are usually not detectable. Like the CIA, the Joint Special Operations Command has become the president’s personal weapon against terrorists, one both Presidents Bush and Obama have wielded often over the years, with little or no input from Congress or the larger public policy community that has weighed in on life-and-death policy options since the beginning on what is now the country’s longest war, the war against al-Qaeda.

JSOC’s parent organization, the U.S. Special Operations Command, located in Tampa, describes the unit’s mission in a deceptively vague way: to “study special operations requirements and techniques… ensure interoperability and equipment standardization.” They decline to offer any more information.

After a JSOC SEAL team killed bin Laden in Pakistan on May 2, 2011, the White House never cracked the door even an inch on this ultrasecret unit, describing them only as “a small U.S. team” and “U.S. military personnel.” The word JSOC was never uttered as details flowed out about the operation. But except for that one time, its operations are never revealed to the media. Its leaders don’t speak in public. Its public affairs officers answer no questions. It has no external website.

The first time I ran into JSOC was in a warehouse on Qatar’s massive air base in the middle of the night in early 2002. I was sitting on a crate next to some army soldiers, waiting for a seat on a cargo plane that would take us to a larger base in Kuwait and then back home to Washington, DC. Three young men with unkempt beards and dirt on their hands came in and sat down. They reminded me of a pack of German shepherd pups, with their boundless enthusiasm for each other and whatever they were up to.

Their name tags were gone, their shoulder patches replaced by blank Velcro. Their uniforms were not quite right, either, and one of them still had a black weapons strap around his thigh. I wanted to ask, “Who the heck are you?” but settled instead for making eye contact with the hope that might lead to a conversation. It didn’t. They looked right past me.

When I got to Kuwait, I described their appearance to an army officer I knew well. “Probably black SOF,” he said.

White SOF I knew. They lived in their own safe houses; regular army soldiers didn’t know much about them, and they worked, in small teams called ODAs, for Operational Detachment-Alphas, in the hinterlands of Afghanistan, Kosovo, and elsewhere. During the initial invasion of Afghanistan, the ODAs teamed up with the remnants of the U.S.-backed Northern Alliance and then rode on horseback with them to call in U.S. air strikes against the Taliban. They had been the first military units on the ground—or so I thought. It took just 316 U.S. Army Special Forces soldiers all of 49 days, with the help of local tribal and warlord forces and U.S. air power, to vanquish the Taliban, recapture Kabul, and chase al-Qaeda into the mountains and across the border into Pakistan. JSOC troops had been there, too, I learned later, serving as bodyguards for the man who would become Afghanistan’s first postwar president, Hamid Karzai, as he moved around the country during the U.S. invasion, and as partners with the CIA paramilitaries working with the Northern Alliance to form a fighting force against al-Qaeda and the Taliban.

Shortly after the invasion of Afghanistan, JSOC troops also took part in the now infamous Tora Bora operation to capture bin Laden. As it turned out, hunting bin Laden and other al-Qaeda leaders was their main mission, and their rules of engagement were carefully and secretly constructed for their use only.

JSOC’s core is built of the army’s Delta Force, Navy SEAL Team 6,2 the army’s 160th Special Operations Aviation Regiment,3 the army’s 75th Ranger Regiment,4 and the air force’s 24th Special Tactics Squadron.5 Its subunits are many, and its task forces are custom-built for a given mission and range in size from a half-dozen to several hundred people.

After 9/11, everything within JSOC grew in size and complexity. It acquired all of the pieces of a self-sustaining secret army, including a personnel pipeline, an equipment and technology acquisition branch, and a research arm. It has its own intelligence division, numbering three thousand staffers who can research and make models of targets, including 3D walk-throughs of locations where JSOC will conduct raids. It has its own drones, its own reconnaissance planes, even its own dedicated satellites in its own space unit. JSOC has its own cyberwarriors, too, who conduct operations like embedding sensors in computer keyboards to follow what suspected terrorists type, or creating fake online identities in order to trap suspects and elicit information. But, most essential to its identity and core mission, JSOC has the rare authority to decide which individuals to add to a kill list, and then to kill them.

JSOC existed for decades before the 9/11 terrorist attacks, but in a much paler form. The idea of a super-elite clandestine force dates from 1977, when Lufthansa Flight 181 was hijacked by four members of the Popular Front for the Liberation of Palestine and was flown to Mogadishu, Somalia. A German antiterrorist squad, GSG 9, stormed the plane and rescued the crew members and passengers with help from Somali commandos. Impressed, the U.S. government took note that it had no similar capability. Months later, a U.S. hostage rescue unit was activated, and spent two years training.

In 1979, soon after it was approved to become operational, a group of Iranian students overran the U.S. Embassy in Tehran and kidnapped its occupants. Five months later, President Carter sent a covert hostage rescue team made up partly of the new unit to bring the Americans home. Operation Eagle Claw, as it was known, instead became an embarrassing failure, defeated by poor planning, bad communications, lack of teamwork between units, a sandstorm, mechanical failure, and a collision of aircraft that killed eight service members and an Iranian civilian. This fiasco led to the creation of the Special Operations Command, a permanent command led by a four-star general or admiral, the highest military rank. The command’s main purpose would be to integrate the various elite forces of the army, navy, and air force charged with freeing hostages, deploying behind enemy lines, and fighting alongside foreign surrogates worldwide on clandestine operations. JSOC would be the only truly clandestine unit of the new command, and it quickly became nearly autonomous from its parent organization.

Prior to the attacks of 9/11, special operations forces were rarely used for counterterrorism operations or manhunting missions. In fact, they were rarely used at all. This was mainly because regular military commanders were suspicious of their independence (General Norman Schwarzkopf famously denied much of a role to special operations for this reason during the first Gulf War, in 1991). But more than that, sending small teams into hostile territory was nearly impossible because the kind of detailed intelligence they would need to operate secretly was always lacking. Neither the mind-set nor the methodology for gathering such information existed in any sophisticated way.

JSOC took its central place in the post-9/11 era under Defense Secretary Donald Rumsfeld, who smarted from the CIA’s ability to move first into Afghanistan and vowed never to be outdone by the agency again. Before he left office, Bush briefly sent JSOC into Pakistan. To soothe the worries of U.S. Ambassador Anne Patterson about the mounting civilian deaths JSOC raids elsewhere had produced, and to prove how carefully its missions were conducted, commanders brought a Predator control console to Patterson’s Islamabad embassy office so she could witness a raid in real time. But the brief forays still became a point of public outcry in Pakistan, and U.S. officials canceled future missions there after only three raids, though the CIA continued to conduct drone strikes.

As the secret organization killed more people and dismantled more terrorist networks, decision makers in Washington gave it more money, more troops, and greater responsibility. Its headquarters doubled in size, as two permanent task forces were established overseas, each commanded by a general officer. From 1,800 troops on September 11, 2001, JSOC grew to a force sometimes as large as 25,000 today. Most of the force provides equipment, logistics, analysis, and everything else needed by the raid parties: the trigger pullers, the snipers, the manhunters.

As JSOC’s role grew more crucial, other organizations that weren’t as lethal or meaningful tried to attach themselves to the organization’s rucksack. It had its pick of partners and swallowed up the ones it wanted. It acquired or teamed up with half a dozen organizations, including the ultrasecret Technical Operations Support Activity, or TOSA6—one of several names for an organization previously known as the Intelligence Support Activity, The Activity, and Grey Fox—which had helped kill drug kingpin Pablo Escobar in Colombia in 1993 and which has its own extraordinary eavesdropping and aviation abilities.

JSOC also partnered with the National Security Agency’s new expeditionary force, with Britain’s SAS,7 and with the special forces equivalents in Jordan, Australia, and Poland, all of whom have taken orders from the Americans, and have also been wounded and killed under their command.

If killing were all that winning wars was about, the book on JSOC would be written. In the first months of the war in Afghanistan, according to senior JSOC leaders who were there, the raid teams killed thousands of people. In the first weeks of the war in Iraq, they helped kill hundreds on the march to Baghdad. As Iraq descended into chaos in the summer of 2005, JSOC leaders pushed their troops to the breaking point to execute 300 raids a month there. As a result, over 50 percent of JSOC Army Delta Force commandos now have Purple Hearts. They were killing dozens and capturing more, and the toll it exacted on the force reminded its commander at the time, General Stanley McChrystal, of Lawrence of Arabia’s description of “rings of sorrow,” the emotional toll casualties took on small groups of warriors. Greatly influenced by Lawrence’s life story, McChrystal thought of his JSOC troops as modern-day tribal forces: dependent upon one another for kinship and survival.

But no war in modern times is ever won simply by killing enough of the enemy. Even in an era of precision weaponry, accidents happen that often create huge political setbacks. In Afghanistan and Pakistan in particular, every JSOC raid that also wounded or killed civilians, or destroyed a home or someone’s livelihood, became a source of grievance so deep that the counterproductive effects, still unfolding, are difficult to calculate. JSOC’s success in targeting the right homes, businesses, and individuals in its prolific night raids was only about 50 percent, according to two senior commanders. Given the difficulty of gathering intelligence on a terrorist and then striking at the moment he is home, commanders considered this rate a good one.

When they made mistakes and the wrong person was at home or the wrong home was invaded, U.S. commanders and civilian leaders, including Presidents Bush and Obama, offered apologies and money, but these measures didn’t neutralize the anti-American feelings the attacks fueled. Eventually, as local folklore grew about men in black with green eyes and laser beams, the commandos’ reputation for violence grew larger than life, and they were blamed for deaths and torture they did not commit. Al-Qaeda and the Taliban were quick to seize on these sentiments and sometimes planted evidence that made JSOC’s raids and mistakes look worse than they were. U.S. diplomats and the regular army troops in daily contact with the people whose countries they occupied were left to soothe tensions, and they were often inadequately prepared for that task.

“Sometimes our actions were counterproductive,” McChrystal told me. “We would say, ‘We need to go in and kill this guy,’ but just the effects of our kinetic action did something negative and they [the conventional army forces that occupied much of the country] were left to clean up the mess.” But such mishaps were considered exceptional; more routine were the invisible successes.

Predictably, as JSOC achievements mounted, the number of private companies working on weapons, sensors, logistics, electronics, and information technology for it soared; a contractor village now hugs the perimeters of JSOC’s North Carolina compound and the Tampa headquarters of the Special Operations Command. By Arkin’s calculation, there are about 5,000 civilian contractors and 49 companies doing top secret work for JSOC: developing unique equipment, conducting primary analysis for targeting, or performing the large administrative tasks required to keep the organization hidden.

JSOC has more eavesdropping and surveillance technology, more translators and cybersnooping equipment, than any clandestine espionage outfit, and yet the White House and the Defense Department do not view it as an espionage organization. Instead, the spying done by JSOC and its member units is called reconnaissance, or “recce” (pronounced “reh-key”) and labeled “intelligence preparation of the battlefield,” which is a way to shoehorn clandestine intelligence-gathering into Title 10 of the U.S. Code,8 the law that governs traditional military activity. Under Title 10, Congress does not have to be briefed on JSOC activities, and JSOC is not considered to be carrying out covert actions, although many people in the CIA and elsewhere think it should be. All traditional espionage and covert operations, usually undertaken by the CIA, are governed by Title 50,9 which requires congressional notification and the involvement of the director of national intelligence. (JSOC’s shutting down of nearly every overseas jihadist website on September 11, 2008, was not considered a covert action, even though it would have been if the CIA had done the very same thing. It was considered a defensive act of war, and thus a traditional military activity.)

In 2003 testimony initially classified top secret, the former Special Operations Command leader General Peter J. Schoomaker told the 9/11 Commission that without precise intelligence, it was impossible for even the best-trained forces to work discreetly abroad. As an example, he told the panel, before 9/11 he had been asked to capture a man leaving Iraq using a small JSOC team. The administration told him, however, that the team could be on the ground for only a short while. The problem, he said, was that no one had a photograph of the man. No one knew what he looked like, what hotel he was supposed to be staying in, or whether he was planning to leave the country by airplane or boat. Schoomaker could launch the mission, he explained, but not with a small team. He would need people at various locations and for a longer period of time to locate the right man. It was the same reason—lack of precise intelligence—that inhibited JSOC from hunting terrorists. Without good information, it was impossible to get close enough to kill or capture them. That is why, up until the 2001 attacks, the weapon of choice against terrorists had either been precision-guided cruise missiles launched from hundreds of miles away or, in even rarer instances, arrest by the FBI for legal trial in the United States when possible.

The 9/11 attacks changed all that. Three days afterward, Pakistani president Pervez Musharraf agreed to allow JSOC to secretly run operations into Afghanistan from Pakistani bases. Oman granted permission to host the unit’s deadly AC-13010 Spectre gunships and rear headquarters, according to an account by army general Tommy Franks, who was in charge of the U.S. military’s first counterattack overseas. In its first post-9/11 iteration, JSOC was a blunt killing machine that paid only moderate attention to the second- and third-order effects of its actions. It pursued al-Qaeda leaders with snipers, helicopter assaults, nighttime raids, and the terrifying AC-130s with side-firing weapons that were a standard part of its assault forces. Its rules of engagement required commandos to announce their presence at raids to give the enemy a chance to surrender; in Afghanistan, though, the men they hunted usually did not surrender, according to commandos who took part in the missions. JSOC’s rules also allowed units to kill civilians traveling with high-value targets, if necessary, which they did quite often in the early days.

Often working with CIA teams, JSOC troops killed hundreds of people in Afghanistan, along the border with Pakistan, and, with the help of indigenous special forces, in the Philippines and elsewhere, according to military officers familiar with JSOC’s operations.

The early lethality of JSOC was demonstrated in the failed December 2001 mountain battle at Tora Bora, in which bin Laden and many of his followers are believed to have escaped across the border into Pakistan. Some fifty JSOC troops of Task Force 11 arrived on December 8 to operate independently of both the overt army Special Operations teams and the Afghan Eastern Alliance. Every night, while Afghan troops and the Special Operations teams accompanying them would withdraw from their forward positions to eat and regroup, JSOC would continue to pummel the 3,000-strong al-Qaeda force. On the nights of December 13 and 14, for example, JSOC killed so many enemy forces that, according to the army’s official history of the war, “dead bodies of al-Qaeda fighters were carted off the field the next day” by the truckload.

On the other side of the border, meanwhile, another JSOC team had its hands full helping Pakistanis round up a large group of al-Qaeda prisoners who had escaped during transport. In that incident, Colonel Michael A. Longoria, commander of the 18th Air Support Operations Group11 assigned to a JSOC task force, facing intense gunfire from snipers and assault by local tribesmen and prisoners, helped a trapped Pakistani convoy fend off the attacks. Longoria killed two enemy snipers, helped recapture the escapees, moved wounded Pakistani casualties, and tended to seventeen dead Pakistani soldiers in what the Pentagon called “the bloodiest escape and firefight in Pakistan during Operation Enduring Freedom.” For his efforts, he was awarded the Bronze Star in a private ceremony.

In contrast to its successes, which usually went unpublicized, JSOC’s mistakes reverberated around the world. In what the Rand Corporation labeled “the single most serious errant attack of the entire war,” on July 1, 2002, a JSOC-operated AC-130 gunship fired upon and killed at least forty-eight civilians in the small village of Kakarak in the Deh Rawod area of Uruzgan province. The incident took many inside the Pentagon by surprise, a senior air force officer said at the time, as most people had already shifted their attention to preparing for war with Iraq. JSOC Task Force 11 had been hunting Taliban leaders in villages seventy miles north of Kandahar in the most intense manhunt since Tora Bora. When a reconnaissance team came under attack, they called for AC-130 gunship support, which subsequently fired on six sites in the vicinity, according to a Pentagon account at the time. The estimates of civilian deaths ranged from forty-eight to hundreds. Villagers told the Washington Post that American soldiers wearing beards came soon after the strikes, inspecting the dead and treating some of the wounded. They said the forces detained seven men and took them away in vehicles with guns mounted on top.

The unclassified summary of the investigation declared the sites hit as “valid targets.” But the report also said that neither the reconnaissance elements nor the AC-130 gunships were initially able to identify who specifically was present at the six targets. From the sky, the summary noted, “it is… not possible to distinguish men from women or adults from children.” The “wedding party incident,” as it became known because a wedding party at one of the six sites was fired upon, came to symbolize American disregard for Afghan civilians. It would be the first American attack to be publicly condemned by President Hamid Karzai. He summoned Lieutenant General Dan McNeill, overall ground commander for U.S. forces in Afghanistan, for an explanation. Secretary Rumsfeld called the incident a “tragedy,” and President Bush “expressed his sympathies” in a telephone conversation with Karzai.

It was the nature of this war, and of the extraordinary freedom offered to JSOC, that this pattern of condemnation and apology would replay itself frequently as the number of lethal operations grew. In 2010, JSOC forces killed five innocent Afghan civilians in another bungled raid. McChrystal’s successor, Vice Admiral William H. McRaven, admitted at the time that his team had committed “a terrible mistake,” and he visited the victims’ relatives to ask for forgiveness. McRaven took two sheep to the village in Paktika province where the raid occurred and offered to sacrifice them in accordance with Afghan tradition. The offer of sacrifice was declined by village elders, but they did accept thirty thousand dollars in cash, according to an eyewitness quoted in the Times of London.

McRaven told the father of two of the victims, “I am a soldier, I have spent most of my career overseas away from my family, but I have children as well and my heart grieves for you.” After the mishap, McRaven ordered that all units use the bright-green laserlike lights on AC-130 gunships that often accompany assault forces on the nighttime raids. While it fractionally reduced the element of surprise, the lights identified the aircraft as American and were often enough to persuade insurgents to give up rather than draw their weapons.

In 2003, JSOC soldiers were among the first troops in southern Iraq, riding in with the protection of an armored task force of the 3rd Infantry Division. According to three senior JSOC commanders, these troops helped the division kill upward of five thousand Iraqis in perhaps the bloodiest portion of the war, the march to Baghdad. “It sounded like World War II, there was so much noise,” said a JSOC commander who was there. The gunners on the armored vehicles faced human waves of Iraqi army forces, fedayeen, and their ragtag civilian supporters. They were ordered to kill anyone who got up on the vehicles. “That’s the dirty little secret, the dark underbelly of the war,” he said. “There were bodies everywhere.” Troops eventually shot dogs to keep them away from the carcasses. Such armored vehicles also delivered the JSOC commandos on their own missions to capture or kill senior Iraqi Baathists loyal to Saddam Hussein and to find and secure weapons of mass destruction that were, it turned out, not there.

While JSOC troops worked well with CIA operatives and analysts in small teams in Afghanistan, the civilian CIA’s inability even with its paramilitary elements to safely move around an increasingly violent Iraq created an intense fissure between the two organizations. JSOC’s relative ease of movement, made possible by the fact that it is a military unit with the best combat training and equipment in the world, and its high enemy-killed-in-action numbers spurred the unit and its civilian supporters in the Pentagon to plan even more missions.

Some of those plans were not without controversy. At the time of General Schoomaker’s testimony to the 9/11 Commission in 2003, just before the war in Iraq began, JSOC and the CIA were in a roiling dispute over whether the military unit could legally conduct missions outside of a war zone and whether the law required the Defense Department, on JSOC’s behalf, to seek permission for these operations directly from the CIA, as the head of the intelligence community. “The bureaucratic mess is onerous,” Schoomaker told the commission, according to a declassified copy of his testimony. Predictably, Schoomaker believed the secretary of defense should have the authority to order clandestine antiterrorism missions.

Unknown to Schoomaker, who had long since ended his career in JSOC, on September 16, 2003, three days before his testimony, Defense Secretary Rumsfeld had signed an order that hit JSOC’s Fort Bragg headquarters like a lightning bolt. Labeled “EXORD”12 and “CJCS War on Terrorism Execute Order,” the approximately eighty-page document created a new category of top secret, compartmented activities, which were to be tightly controlled under the code name Focal Point. These were aimed at disrupting, capturing, and destroying the al-Qaeda network and its supporters anywhere in the world. In military terms, it was the equivalent of a Presidential Finding, the written rationale and approval the president was required to send to Congress when authorizing a CIA covert action. There was one big difference: JSOC would not need to notify Congress because, its lawyers argued successfully, it conducted traditional military operations with a traditional chain of command—no matter how untraditional its operations appeared.

The EXORD listed fifteen countries where these operations could occur. Next to each country was a list of activities permitted under various scenarios with the preapprovals needed to carry them out. In Iraq and Afghanistan, where declared wars were under way, authority to prepare for and take lethal action against al-Qaeda members was granted without additional approval from the president or secretary of defense. In the other countries in which they might operate—among them Algeria, Iran, Malaysia, Mali, Nigeria, Pakistan, the Philippines, Somalia, and Syria—JSOC forces would, in most cases, need at least tacit approval from the country involved, and a sign-off from some higher authority in its chain of command. In the Philippines, for example, JSOC could undertake psychological operations to confuse or trap al-Qaeda operatives but would need approval from the White House for lethal action. To attack targets in Somalia required at least approval from the secretary of defense, while attacks in Pakistan and Syria needed the president’s sign-off.

The EXORD also included a lengthy description of the rules of engagement for each scenario, including which types of munitions and electronic surveillance should be used for nighttime and daytime assaults, and what extra care was required to minimize the possibility that civilians would be killed or injured. Assaults likely to result in large numbers of civilian casualties needed increasingly higher levels of approval.

Creation of the EXORD had taken many months and dozens of meetings between the various, and jealously competitive, national security agencies. The CIA didn’t want JSOC encroaching on its turf; the State Department was worried about the ramifications to diplomatic relationships if these missions went awry or were somehow discovered and made public. But with Bush’s full support, Rumsfeld signed off and the other agencies relented. The next day, when the order became official, JSOC began its journey toward superseding the CIA as the center of an opaque universe, the dark matter that would shape the global war against al-Qaeda and, in the process, mold relations between countries.

By then it was mid-2003, the hunt for bin Laden was going nowhere, and Iraq was in the hands of the coalition. Major General Dell Dailey, the JSOC commander at the time, worried about the toll of constant overseas deployment on such an elite, ever-ready unit. He proposed decreasing the number of forces overseas: bringing them home, where they would be ready to surge into hot spots when needed. McChrystal, then on the Joint staff, listened in silence as Dailey spoke to the chairman of the Joint Chiefs. Three months later, when he became JSOC’s new commander, McChrystal immediately reversed course, and JSOC would never be the same.

McChrystal had learned a lot about Washington from his work as the vice chief of operations on the Joint Staff. He had been shocked by the acrimony between Rumsfeld and some generals on the Joint Staff and between the various intelligence and military organizations all trying to accomplish the same things. He decided there was a natural aversion to decision making at the top of government. No one wanted to be wrong, so they either asked more questions or added more layers to the process, sometimes without even realizing it. The result was that the process of getting approval for action slowed to a crawl.

The buzzwords after 9/11 had been “sharing” and “interagency cooperation.” But those were just words. Practically, it meant the meetings were bigger and longer and, given the increased compartmentalization, included people who either couldn’t actually talk to each other or were mutually in the dark about essential details, making the process less productive than it should have been. Also, any one of a multitude of agencies could stifle action until it was too late. Top Secret America, in other words, had become inert under its own weight and size.

Although JSOC’s new power had come from Washington, McChrystal believed that in order to be successful, he had to move it as far away from the capital as possible, “to slip out of the grip” of Washington’s suffocating bureaucracy, he told associates.

Under McChrystal, JSOC would become the adaptable, innovative counterterrorism organization that Top Secret America was supposed to be, too. He embraced the new freedoms the White House had given to its secret units to aggressively target individuals from the air or with raids on the ground. But he achieved this only by outright rejecting at least four of Top Secret America’s defining characteristics: its enormous size, its counterproductive duplication, its internal secrecy, and its old-fashioned, hierarchical structure.

During McChrystal’s first orientation trip overseas, in October 2003, the new JSOC commander found 20 of his men in Afghanistan conducting occasional raids, and 250 men in Iraq who, using one surveillance drone, were trying to find Saddam Hussein and his loyalists. He flew by helicopter from Baghdad to Mosul and Ramadi, where several other JSOC troops were stationed in virtual isolation. His 12 men in Mosul, he discovered, were totally cut off from the others, with no effective way to communicate or to share information about the enemy. And there was no way to stay on top of what the CIA or embassy staff was working on.

“We needed to become networked together,” he said in an interview. To make this happen, he began a campaign to coax other agencies to help him out, and to acquire the technology, and force the cultural change, to make this possible. McChrystal eventually moved his headquarters to Balad Air Base, forty-five miles northeast of Baghdad, and worked inside an old concrete hangar that had once housed Saddam Hussein’s fighter jets. There he constructed a warren of three connecting command centers: one dedicated to fighting al-Qaeda in Iraq, one dedicated to fighting the Shi’a extremists in Iraq (established only in 2006), and a third for himself, so he could oversee JSOC’s worldwide operations, including those in Afghanistan.

Inside, young techies from the National Security Agency and their peers from the National Geospatial-Intelligence Agency worked alongside old hands from the State Department and the CIA and starched FBI agents deployed to gather evidence and keep it untainted from the chaos of battle for use in Iraqi courts. Computer screens hung from the ceiling, some of them replaying footage of the falling World Trade Center towers for motivation. Photos of the faces of wanted terrorists were tacked to the walls. Everyone had the necessary clearances, and, with McChrystal’s prodding, they talked to each other—which meant they could actually get some work done.

For some inside government, this emphasis on sharing information and brainstorming problems as a group might have been seen as pie-in-the-sky thinking, a kumbaya kind of notion. But McChrystal was anything but a kumbaya type of leader. His legend preceded him. Stories were passed that he ate just one meal a day and ran at least ten miles every day. He was impatient, chewed his nails, was intolerant of sloppiness, got bored easily. He certainly looked the part of the manic commander, with his taut, bony face, intense eyes, and thin physique. Shortly after his arrival in Balad, a sign went up inside the wire: “17-5-2.” This was McChrystal’s prescription for time management: seventeen hours for work, five hours for sleep, two hours for eating and exercise. Three meals a day meant twenty minutes for each, one hour to exercise, and another to clean up and organize. That was it.

When McChrystal addresses civilian audiences now, he sometimes begins by showing a photograph of his father, General Herbert J. McChrystal Jr., “the soldier I wanted to be.” McChrystal was the fourth in a family of five boys and one girl. All Herbert’s children grew up to serve in the military or marry into it. McChrystal graduated from West Point in 1976, during the army’s post-Vietnam crisis, and after that ascended through the ranks of the elite, secretive wing of Special Operations. He served as a staff officer and an operations officer in the first Gulf War and spent time on a fellowship at Harvard University and the Council on Foreign Relations in New York, where he ran a dozen miles each morning to its Upper East Side offices.

Mixed with his legendary work ethic was his Scotch Irish exuberance and common-man demeanor. He seemed almost naïvely trusting (which would become his undoing years later, after he and his staff made inappropriate comments about his civilian leaders to a Rolling Stone magazine reporter; he offered to resign, and Obama accepted). He viewed beer calls with subordinates as an important bonding exercise. He made people call him by his first name. He told them what he thought. “When I asked him a question, he actually gave me an answer,” said one of his top advisers, Graham Lamm, a Brit. He told people that he considered his Ranger vow never to leave a fallen comrade behind more binding even than his marriage vows. His colleagues both civilian and military describe him as a force of nature, a personality so strong and persuasive that he convinced his ever-widening circle of teammates that to be successful would mean casting off another trademark of Top Secret America—its compartmented secrecy.

Within the confines of this highly classified world, McChrystal exposed the guts of his operation to everyone involved in it. His subordinates learned to share information with one another because he ordered them to do so. Sharing, he told them, made it more likely that the organization would function better. “The more people you shared your problem with, the better you’d do in solving it,” he would say.

To push this idea further, McChrystal ordered the creation of what became a simple PC-based common desktop and portal where troops could post documents, conduct chats, tap into the intelligence available on any target—pictures, biometrics, transcripts, intelligence reports—and follow the message traffic of commanders in the midst of operations. By the summer of 2004 it was in place. Now, not only would every single troop in JSOC have access to this real-time picture of evolving targets on the battlefield, but so would the unit’s historical rivals: the CIA, the NSA, the FBI, the Defense Intelligence Agency, and even certain elements within the State Department, including several ambassadors with whom McChrystal worked closely. He wanted them all to become a part of the JSOC intelligence-gathering apparatus and was willing to show enough of his hand to convince them to come along.

The goal of such an integrated process was overdue by the time McChrystal took command of the relatively small JSOC corner of Top Secret America. While much of the lumbering intelligence community in Washington continued along its dysfunctional path, McChrystal began salting every relevant national security agency in the capital region with JSOC liaison officers. These were not members of the B Team, as they were in many organizations—they were the smartest, most worldly troops in the unit, and sometimes even its most senior. For example, when relations between the CIA and JSOC were rough in the beginning of the Iraq deployment, McChrystal gave the agency his chief intelligence officer, Colonel Michael Flynn, to work in the Baghdad station.

McChrystal made sure that all the key administration and DoD players had a JSOC liaison on their personal staff, including Richard Myers, chairman of the Joint Chiefs of Staff; CIA director George Tenet; General John Abizaid, commander of the Central Command; Ryan Crocker, U.S. ambassador to Afghanistan; and Anne Patterson, U.S. ambassador to Pakistan. In all, McChrystal pushed out more than 75 liaison officers to Washington and another 100 in the field. They rotated every four months so none would become bureaucrats, disconnected from combat.

For the most part, McChrystal’s liaison offensive worked as intended, though there were some in the target organizations who did not appreciate the gesture, and thought of the liaisons as spies for an organization that was already too important. Nevertheless, those suspicions did little to derail JSOC’s spectacular rise. Even the nature of the new war contributed. The Iraq conflict’s heavy reliance on modern technology gave tech-savvy JSOC teammates an advantage they did not have in Afghanistan, where few people used cell phones, laptop computers, or even landline telephones, all devices that JSOC, with the help of the National Security Agency and TOSA, would eventually learn to monitor and locate. Before the Iraq push, the NSA was focused on tracking movements and conversations of world leaders and key terrorists to learn their plans and intentions, not on tracking single individuals on the battlefield simply to discover their location. It rarely shared the raw product of its monitoring directly with combat units—that, it was felt, was the job of the service-level military intelligence units. But the NSA wanted in on the action, too, and soon was sending representatives to McChrystal’s Balad headquarters.

The collaboration paid off handsomely. By September 2004, the NSA had figured out how to geolocate cell phones even if they were off. “We just had a field day,” said a senior JSOC commander. “We did thousands of them.” When they hit on a hot phone—“The Find,” as they called it—someone could send a plane to watch the building where the phone had lit up, and a raid would be mounted if appropriate. Using a new computer linkup called the RTRG,13 for Real Time Regional Gateway, they would feed in every bit of data or piece of paper they captured and would soon get back a set of new phone numbers and new leads.

Lacking actual informants and eyes on the ground, aerial surveillance of the enemy became the primary means of tracking terrorists and Saddam loyalists. Lacking enough aircraft and impatient with Washington’s acquisition process, McChrystal’s team improvised. They turned two captured four-seater Pilatus aircraft that had been used for drug smuggling into camera surveillance planes. They mounted cameras on their UH-60 helicopters and on a DH-7 leased aircraft. They cajoled six planes out of the National Guard, outfitted them with sensors, and began using them, too. Their surveillance fleet, a hodgepodge of fifteen types of aircraft, grew from one aircraft to forty in a matter of a year or so.

Another tool they perfected was the use of dogs before and during raids. They rigged cameras on the animals’ backs and trained them to run a perimeter or through a house or compound fast enough to avoid being shot. “They were fearless,” said one senior JSOC commander. They would go down holes, point out trip wires, sniff out explosives, pick up the scent of humans; the dogs even learned to fast-rope out of helicopters harnessed to their handlers and to do parachute jumps in tandem with them. Some were killed, and others were wounded multiple times. The commandos nominated several for Purple Hearts, and when officials denied them real medals, they created their own version to honor their canine teammates.

Most Afghans and Iraqis feared dogs. Their presence was almost as controversial as drones, and Afghan president Hamid Karzai complained bitterly about the animals. Once he even called Secretary of State Hillary Clinton as she flew across the globe to tell her that one had bitten a young boy. “We’re keeping the dogs,” she brusquely told him, according to one person who overheard the conversation.

The early 2000s were a period of rapid commercial invention inside Top Secret America; many accessories for America’s high-tech war were introduced: drones as small as dragonflies, robots of astonishing variety, sensors that could be implanted somewhere and spew out information about nearby movements for as long as a year, tiny radio and computer sets and miniature tracking devices that could pinpoint the location of individual soldiers wherever they were in the world.

One of the most useful innovations was what some in JSOC dubbed the Electronic Divining Rod, a sensor worn by commandos that could detect the location of a particular cell phone. Wearing the device, JSOC troops entering an apartment building, for example, could follow the beeping noise from the monitor into a room full of people. Like a coin-sweeper used on the beach, the device would get louder as the soldier carrying it came closer to the person carrying the phone in question.

Killing the enemy was always the easy part, JSOC commanders said; finding him was the hard part. But thanks to a man named Roy Apseloff, JSOC’s intelligence collection improved dramatically. Apseloff, who had introduced himself to McChrystal and his chief intelligence officer, Michael Flynn, one day when they were visiting CIA headquarters, managed a small office called the National Media Exploitation Center, located in an odd-shaped building in Fairfax, Virginia. He explained how he could help them mine and analyze the pocket litter—literally, the trash in a suspect’s pockets—as well as documents and electronic equipment his troops were seizing in raids.

At the time, these items were bagged up and left for translators to work on in their spare time. Apseloff, however, showed McChrystal and Flynn how his team of thirty people, using special technology to download the contents of locked and/or damaged computers, could extract names, phone numbers, messages, and images, and then, using specialized software, could process and store that data and link it to other information—information that might help analysts find not just one more bad guy but an entire network of them. McChrystal and Flynn were impressed, and a long, close partnership began.

The major challenge McChrystal and Apseloff confronted was how to find the gems in the trash quickly enough to be useful. This was an old problem. What was about to change was the speed with which connections could potentially be made. The time between the capture of information and its interpretation had been reduced from weeks in World War II, to days in the first Gulf War, to hours in Kosovo, to minutes and even seconds in Afghanistan and Iraq.

The key was more bandwidth, the size of the electronic pipeline that carried information like email and telephone calls around the world. In transcontinental communications, bandwidth can be increased in only two ways. A pipeline for digital information can be laid under the ocean floor in the form of a glass-filled fiber-optic cable, or it can be built in the sky using an orbiting satellite to receive the information on its way up from one spot and beam it back down to another, often in another country. Both pipelines are expensive to build and inherently limited in how much they can carry—the satellite method especially so.

The value of bandwidth was first realized during the Kosovo air war in 1999, when commanders began using video-teleconferencing to allow communication between participants in different countries and on ships at sea, and when Predator drones mounted with cameras were first used to film Serb paramilitary forces on the ground. To reposition the finite number of military satellites available so that they could transmit information from Kosovo required borrowing the digital pipelines used by other military commands, such as those the Pacific Command used to track the civil war in East Timor and missile developments in China and North Korea. Ever since, vicious battles have been waged between the military services and individual commanders over bandwidth access.

Luckily for the military, the attacks of 2001 coincided with an entirely unrelated economic development: the dot-com bust. The economic downturn created a glut in commercial satellite pipelines already available and now underutilized. The military quickly bought up private companies’ excess capacity, which only fed its craving for more and more information requiring ever more capacity.

According to commanders, in the early days of the Afghanistan war, the Special Operations Command, including JSOC, spent $1 million a day on commercial bandwidth. Within a year after McChrystal’s arrival, JSOC had linked sixty-five stations around the world to enable viewers to participate in the twice-daily, forty-five-minute video teleconferences that he held. By 2006, JSOC had increased its bandwidth capability by one hundred times what it had been just three years earlier, according to senior leaders. All that information flowing through the pipeline wasn’t just sent to Washington; it was also pushed down to Delta Force troops, Navy SEALs, and the 160th Night Stalker pilots at their bases around Afghanistan and Iraq.

The other challenge JSOC faced was a human one: how its troops were interrogating and treating detainees. Shortly after McChrystal took command in September 2003, he visited the JSOC detention facility in Iraq, a place separate from the larger Abu Ghraib prison that would become notorious for prisoner abuse at the hands of low-level army soldiers. There was a skeletal staff of about thirteen people, meaning they had no time to try to cajole detainees into divulging important intelligence. There was little or no information about individual detainees for interrogators to use to question them in a more productive way. As a result, interrogators didn’t know what questions to ask or how to ask them to get a response.

Worse, some JSOC Task Force 121 members were beating prisoners—something that would before long become known to Iraqis and the rest of the world. Indeed, even before the Abu Ghraib prison photos began circulating among investigators, a confidential report warned army generals that some JSOC interrogators were assaulting prisoners and hiding them in secret facilities, and that this could be feeding the Iraqi insurgency by “making gratuitous enemies,” reported the Washington Post’s Josh White, who first obtained a copy of the report by retired colonel Stuart A. Herrington.

That wasn’t the only extreme: in an effort to force insurgents to turn themselves in, some JSOC troops also detained mothers, wives, and daughters when the men in a house they were looking for were not at home. These detentions and other massive sweep operations flooded prisons with terrified, innocent people—some of them were more like hostages than suspects—that was particularly counterproductive to winning Iraqi support, Herrington noted.

Another investigation of JSOC detention facilities in Iraq during a four-month period in 2004 found interrogators gave some prisoners only bread and water, in one case for seventeen days. Other prisoners were locked up for as long as seven days in cells so cramped they could not stand up or lie down while their captors played loud music to disrupt sleep. Still others were stripped, drenched with cold water, and then interrogated in air-conditioned rooms or outside in the cold.

As the Iraqi insurgency intensified and pressure mounted to stop it, JSOC interrogators converted one of Saddam Hussein’s torture cells—complete with eighteen-inch hooks attached to the ceiling—into a jet-black, garage-sized interrogation booth they named the Black Room. There, according to the New York Times, interrogators beat some prisoners with rifle butts, spit in their faces, and used them for target practice in a game of paintball. Posters at the center advised, “NO BLOOD, NO FOUL,” meaning interrogators couldn’t be prosecuted if they didn’t make a prisoner visibly bleed. The CIA and FBI were concerned enough about the tactics that they barred their own personnel from participating in JSOC interrogations. The Special Operations Command disciplined thirty-four JSOC task force soldiers involved in five cases over a one-year period beginning in 2003.

McChrystal’s first tour of the Baghdad detention center shocked him. Several detainees were being kept naked, and dogs were being used to guard their cells. “This is how we lose. This is our Achilles’ heel,” he told associates.

In response, McChrystal set out to professionalize the interrogation system by training interrogators how to best question prisoners and by teaching others how to collect information about a detainee and the details of his capture to prepare for the first interrogation session. By the summer of 2005, JSOC had what Michael Flynn once called “industrial-scale, capture-interrogation-exploitation operations.” Interrogation booths at Balad were just around the corner from the large warren of rooms where specialists mining thumb drives, computers, cell phones, documents, and translations of other interrogations sat. Twenty people were tasked with collecting and analyzing the information needed to effectively interrogate a single detainee. Flynn insisted that the assault leader join the interrogation team of each detainee he captured, ensuring that someone who knew precisely who had been found in which room of each house and with what evidence—cell phones, CDs, and so forth—could determine what incriminating piece of evidence belonged to whom.

The army’s technical paper maps were torn down from the walls of the Balad command center and replaced with flat-panel screens and Google Earth–type maps. Detainees willing to cooperate were taught how to use a mouse to fly around their own virtual neighborhoods; some became so fascinated with the technology that they would eagerly zoom in and out of streets and buildings, showing interrogators safe houses, weapons caches, and back alleys.

Egyptians and Saudis were occasionally brought in to interrogate their own nationals, to more easily appeal to them in their own dialect and culture. Family members were connected by videoconferencing to help convince their sons or brothers to cooperate. When the foreign delegations balked at returning, video-teleconferencing was set up so a prisoner could be questioned and pressured by someone back home. Following McChrystal’s crackdown, JSOC still had to use the rules laid out in the Army Field Manual to interrogate detainees; but its interrogators were permitted to keep them segregated from other prisoners and to hold them, with the proper approvals from superiors and sometimes Defense Department lawyers, for up to ninety days before they had to be transferred into the regular military prison population. They still are permitted to do so.

The new interrogation system included an FBI and judicial team that put together evidence needed for trial by the Iraqi Central Criminal Court in Baghdad. From early 2005 to early 2007, the teams sent more than 2,000 individuals to trial, said several senior military officials.

The U.S. military and JSOC were not the only organizations that had invaded Iraq. Al-Qaeda was quick on their heels. Al-Qaeda used the U.S. invasion of Iraq as a call to arms to terrorists and recruits throughout the Middle East who flooded in from Tunisia, Libya, Egypt, and Saudi Arabia—as many as two hundred of them a month at the high point. They set up safe houses from al-Qa’im, on the Syrian border, to Baqubah, northeast of Baghdad, Fallujah, and Ramadi. Realizing that it wasn’t necessary to risk another attack inside the United States, the terrorists hoped to defeat the enemy in a land whose culture and language these foreigners, they assumed, couldn’t begin to understand. Saddam Hussein had been decidedly secular in orientation, his regime unfriendly to groups like bin Laden’s. Now with Saddam gone and the country in chaos, al-Qaeda moved to fill the vacuum. Thus JSOC’s mission, in part, became solving a problem in Iraq that President Bush’s decision to invade had actually created.

Having been surprised to discover, following the initial invasion, that there were no al-Qaeda in Iraq, military commanders were reluctant to believe it when operatives actually did arrive in force several years later. By then JSOC had discovered hard evidence that an intricate terrorist web actually existed and was mounting continuous, deadly operations against the Iraqi population and American troops. Their evidence was gathered using a combination of the rapid analysis of material seized in raids and more effective, less coercive interrogation methods, with one set of detainees leading to another set of operations, which led to more captures and more detainee interrogations. By the end of 2005, a shocking picture emerged: Iraq was infested with semiautonomous but highly organized al-Qaeda networks. There was one in the Ramadi-Fallujah area; another along the Tigris River Valley, another in Mosul; another in Haditha and al-Qa’im. Al-Qaeda had divided Iraq into sections and put a provincial commander in charge of each. That commander further divided his territory into districts and put someone in charge of each of those, too. There were city leaders within those areas, and cells within each city. There were leaders for foreign fighters, for finance, and for communications, too.

In the spring of 2006, using the magic of bandwidth and the constant surveillance of unmanned aircraft, JSOC executed a series of raids, known to troops as Operation Arcadia, in which they collected and analyzed 662 hours of full-motion video shot with more than one aircraft flying overhead at all times over seventeen days (almost 40 hours analyzed for each 24-hour period). They also netted 92 compact discs, twelve SIM cards, and barrels full of paper. Those finds led to another round of raids at 14 locations. Those raids yielded 14 hard drives, 11 thumb drives, and a basement stacked with compact discs, 704 of them, including a representation of the entirety of al-Qaeda’s sophisticated marketing campaign (it included pictures of civilians wounded or killed by what the organization asserted were American actions). It was all a precursor to the capture of Iraq’s top al-Qaeda operative, Abu Zarqawi, by JSOC’s Delta Force on June 7, 2006.

During this time, JSOC’s Balad headquarters was busier than ever before and included nearly 100 CIA employees and 80 from the FBI. JSOC’s EKIA (enemy killed in action) list grew longer, too. In 2008, in Afghanistan alone, they struck 550 targets and killed roughly 1,000 people, along with 17 civilians. In 2009, they executed 464 operations and killed 400 to 500 enemies, some al-Qaeda but mostly Taliban, according to internal sources.

Because of JSOC’s many successes on the battlefield, the Defense Department gave the unit a bigger role in several nonmilitary assignments as well. JSOC worked to trace the secret flow of money from international banks to finance terrorist networks. It became deeply involved in “psychological operations,” which later became “military information,” because it sounded less intimidating. JSOC sent small teams of soldiers out of uniform into embassies around the world to help with what it called media and messaging campaigns. With a formidable production unit at its North Carolina headquarters, it could build websites whose U.S. sponsorship was sometimes obscured. It could distribute cell phones and radios to friendly forces, create magazines and video programs, and produce radio programs for broadcast into any country in the world, including those that actively seek to jam outside communications.

When Obama came into office, he cottoned to the elite organization immediately. (It didn’t hurt that his CIA director, Leon Panetta, has a son who, as a naval reservist, had deployed with JSOC.) Soon Obama was using JSOC even more than his predecessor to conduct secret targeted killing of al-Qaeda and Taliban leaders in Afghanistan and elsewhere, primarily Pakistan and Iraq. In 2010, Obama secretly directed JSOC troops to Yemen to kill the leaders of al-Qaeda in the Arabian Peninsula. Several dozen troops were sent over a six-month period to kill scores of people on JSOC’s hit list, among them six of the fifteen individuals U.S. intelligence had identified as top regional commanders.

In Yemen, JSOC joined an interagency team, led by the ambassador, and including the CIA. U.S. troops did not take part in any actual raids but helped plan missions, developed tactics, and provided U.S. weapons and munitions. They also shared some of the most sensitive electronic and video surveillance, as well as three-dimensional terrain maps.

Cooperative efforts with Yemen to fight terrorism dated from the attacks of 2001, when CIA director Tenet coaxed Yemeni president Abdullah Saleh into a partnership that would permit the CIA and military units to hit Yemeni terrorist training camps and al-Qaeda targets. Saleh agreed, in part because he believed his country, the ancestral home of Osama bin Laden’s father, was next on the U.S. invasion list, according to an adviser to the Yemeni president. Tenet gave Saleh’s forces helicopters, eavesdropping equipment, and 100 Army Special Forces to train an antiterrorism unit. American commandos also crafted a media campaign in support of Saleh that portrayed him as an anticorruption activist, giving rise to a certain irony by mid-2011, when the Arab Spring forced him into exile, in part because of his corrupt ways. Saleh used the campaign without attribution to its U.S. authors before the elections, though the messages did not overtly ask citizens for their vote; that kind of political campaigning could only be carried out by the CIA, because secretly influencing the politics of another country is considered a covert action.

Besides deepening the secret relationship with Yemen, Obama sent JSOC forces elsewhere as well. A helicopter assault force was deployed to Somalia to kill Saleh Ali Saleh Nabhan, who was involved in several bombings in Kenya, including the attack on the U.S. Embassy in 1998.

Obama’s national security team worked in secret to maintain and deepen the bilateral intelligence relations forged in Yemen during the era of CIA director George Tenet. A steady stream of high-ranking officials visited the president beginning in 2010. In April, Saleh boasted on his government’s official website of a visit by JSOC commander McRaven, who was rarely seen in public. Saleh’s government posted a photo of a meeting on its official website as proof. The unacknowledged JSOC was stunned by the announcement.

When Yemeni citizens joined the Arab Spring, JSOC was forced to cease operations while the chaos settled. Having backed Saleh, an autocrat who was ruthless with political opponents, the U.S. government had to suspend its actions, too, and wait out the shake-up.

“I don’t think it’s my place to talk about internal affairs in Yemen,” Defense Secretary Robert Gates told reporters traveling with him in Moscow in March 2011. “We are obviously concerned about the instability in Yemen. We consider al-Qaeda in the Arabian Peninsula, which is largely located in Yemen, to be perhaps the most dangerous of all the franchises of al-Qaeda right now. So instability and diversion of attention from dealing with AQAP is certainly my primary concern about the situation.”

With so many new targets and so many target packages awaiting execution, the frustration inside JSOC mounted as turmoil from the Arab Spring forced the president and his clandestine commandos to be patient. In the meantime, the organization turned its attention elsewhere and continued its march ahead of the rest of Top Secret America: in a thirty-thousand-square-foot office building turned command center, JSOC began to replicate the intelligence analysis and targeting model that had worked so well in Afghanistan, Iraq, and Yemen to fight one of its most recalcitrant foes.

The intelligence team was assembled. So was the target development group and envoys from the CIA, the FBI, the NSA, the Defense Department, and the National Media Exploitation Center, the facility that was so helpful to McChrystal when he was beginning the secret unit’s transformation eight years ago. This task force is not located in a former dictator’s bunker or in some godforsaken part of the world. It is across the highway from the Pentagon in pristine suburban splendor, near a popular buffalo burger restaurant and a five-minute drive from McChrystal’s home office and the former general’s favorite beer call restaurants.

As its name implies, the focus of Joint Special Operations Task Force–National Capital Region (JSOTF-NCR) is not the next terrorist network to have sprung up in some far-off corner of the world but another of JSOC’s lifelong enemies: the Washington bureaucracy. Some fifty battle-hardened JSOC warriors and a handful of other federal intelligence and law enforcement agencies work in the operations center every day. Its mission is to replicate McChrystal’s model for operations under consideration in other countries.

Mexico is top on its list of priorities. JSOC is eager to apply its targeted killing model—with night raids and armed drone attacks—to help destroy the drug and weapon networks worming their way into the United States and infecting Mexico’s political and social fabric. Although the CIA is leading a quickly expanding counternarcotics effort there, so far the Mexican government, whose constitution limits contact with the U.S. military, is relying on the other federal agencies—the CIA, the DHS, the Drug Enforcement Agency, and Immigration and Customs Enforcement (ICE)—for intelligence collection, fusion, analysis, intercepts, surveillance, targeting, equipment, and training to help them stop the cartels. More aggressive proposals, including some that would allow the CIA and JSOC to help the Mexican government conduct targeted killings, have been discussed at the White House, Langley, and the Pentagon, and in other offices of Top Secret America.

But JSOC’s National Capital task force is not just sitting idly by, waiting to be useful to its southern neighbors, either. It is creating targeting packages for domestic U.S. agencies that have sought its help. It has put together plans for raids and investigations for the U.S. Immigration and Customs Enforcement agency, which is the latest federal agency to make a big play for a larger counterterrorism role. ICE plans to use its vast number of U.S. law enforcement authorities and its contacts in immigration detention jails and smuggling pipelines. The second largest federal law enforcement group in the nation, ICE increased the number of its counterterrorism investigations and arrests in 2011, making a run at what had been the FBI’s sole purview. Not surprisingly, it was doing so on its own, without coordinating with the bureau.

JSOC has brought the data mining that was so helpful to making lightning-fast raids overseas to its work for U.S. federal agencies. The National Capital task force has its own supercomputer that can crunch billions of data points to narrow searches for particular people, telephone numbers, and locations of interest. Its database includes numbers from nearly every U.S. phone book, as well as commercially available data on U.S. citizens and residents. To abide by rules limiting the military’s access to information on Americans, the computer automatically masks the identity of any U.S. citizen or resident from the gaze of its military operators. That information can only be unmasked in certain circumstances permitted under U.S. law, said military and law enforcement officials. JSOC, which for so long stayed as far away from Washington as possible, has arrived in force to take on the slow metabolism of Top Secret America’s obese body, to infiltrate its command and control centers, to push its leaders to make decisions that use JSOC’s unique skills, and to be ready to pounce anywhere in the world once they do.