The CIA’s armed drones and paramilitary forces have killed dozens of al-Qaeda leaders and thousands of its foot soldiers. But there is another mysterious organization that has killed even more of America’s enemies in the decade since the 9/11 attacks.

Members of an Army Special Forces team work as part of a combined JSOC task force in the Baghdad area in mid-2007. Their mission was to train Iraqi counterterrorism troops and to work with them on night raids aimed at capturing key Iraqi insurgents and al-Qaeda members. (Chief Mass Communication Spec. Michael B.W. Watkins / U.S. Navy) CIA operatives have imprisoned and interrogated nearly 100 suspected terrorists in their former secret prisons around the world, but troops from this other secret organization have imprisoned and interrogated 10 times as many, holding them in jails that it alone controls in Iraq and Afghanistan.

Since the Sept. 11, 2001, attacks, this secretive group of men (and a few women) has grown tenfold while sustaining a level of obscurity that not even the CIA managed. “We’re the dark matter. We’re the force that orders the universe but can’t be seen,” a strapping Navy SEAL, speaking on the condition of anonymity, said in describing his unit.

The SEALs are just part of the U.S. military’s Joint Special Operations Command, known by the acronym JSOC, which has grown from a rarely used hostage rescue team into America’s secret army. When members of this elite force killed Osama bin Laden in Pakistan in May, JSOC leaders celebrated not just the success of the mission but also how few people knew their command, based in Fayetteville, N.C., even existed.

This article, adapted from a chapter of the newly released “Top Secret America: The Rise of the New American Security State,” by Washington Post reporters Dana Priest and William M. Arkin, chronicles JSOC’s spectacular rise, much of which has not been publicly disclosed before. Two presidents and three secretaries of defense routinely have asked JSOC to mount intelligence-gathering missions and lethal raids, mostly in Iraq and Afghanistan, but also in countries with which the United States was not at war, including Yemen, Pakistan, Somalia, the Philippines, Nigeria and Syria.

“The CIA doesn’t have the size or the authority to do some of the things we can do,” said one JSOC operator.

The president has also given JSOC the rare authority to select individuals for its kill list — and then to kill, rather than capture, them. Critics charge that this individual man-hunting mission amounts to assassination, a practice prohibited by U.S. law. JSOC’s list is not usually coordinated with the CIA, which maintains a similar, but shorter roster of names.

Created in 1980 but reinvented in recent years, JSOC has grown from 1,800 troops prior to 9/11 to as many as 25,000, a number that fluctuates according to its mission. It has its own intelligence division, its own drones and reconnaissance planes, even its own dedicated satellites. It also has its own cyberwarriors, who, on Sept. 11, 2008, shut down every jihadist Web site they knew.

Obscurity has been one of the unit’s hallmarks. When JSOC officers are working in civilian government agencies or U.S. embassies abroad, which they do often, they dispense with uniforms, unlike their other military comrades. In combat, they wear no name or rank identifiers. They have hidden behind various nicknames: the Secret Army of Northern Virginia, Task Force Green, Task Force 11, Task Force 121. JSOC leaders almost never speak in public. They have no unclassified Web site.

Despite the secrecy, JSOC is not permitted to carry out covert action like the CIA. Covert action, in which the U.S. role is to be kept hidden, requires a presidential finding and congressional notification. Many national security officials, however, say JSOC’s operations are so similar to the CIA’s that they amount to covert action. The unit takes its orders directly from the president or the secretary of defense and is managed and overseen by a military-only chain of command.

Under President George W. Bush, JSOC’s operations were rarely briefed to Congress in advance — and usually not afterward, either — because government lawyers considered them to be “traditional military activities” not requiring such notification. President Obama has taken the same legal view, but he has insisted that JSOC’s sensitive missions be briefed to select congressional leaders.

Lethal force

JSOC’s first mission in 1980, Operation Eagle Claw, an attempted rescue of diplomats held hostage by Iranian students at the U.S. Embassy in Tehran, ended in a helicopter collision in the desert and the death of eight team members. The unit’s extreme secrecy also made conventional military commanders distrustful and, as a consequence, it was rarely used during conflicts.

Defense Secretary Donald Rumsfeld, smarting from the CIA’s ability to move first into Afghanistan and frustrated by the Army’s slowness, pumped new life into the organization. JSOC’s core includes the Army’s Delta Force, the Navy’s SEAL Team 6, the Air Force’s 24th Special Tactics Squadron and the Army’s 160th Special Operations Aviation Regiment and the 75th Ranger Regiment.

The lethality of JSOC was demonstrated in the December 2001 mountain battle at Tora Bora. Although bin Laden and many of his followers eventually escaped across the border into Pakistan, an Army history said that on the nights of Dec. 13 and 14, JSOC killed so many enemy forces that “dead bodies of al-Qaeda fighters were carted off the field the next day” by the truckload.

It also made mistakes. On July 1, 2002, in what the Rand Corp. labeled “the single most serious errant attack of the entire war,” a JSOC reconnaissance team hunting Taliban came under attack and an AC-130 gunship fired upon six sites in the village of Kakarak . The estimates of civilian deaths ranged from 48 to hundreds. The “wedding party incident,” as it became known because a wedding party was among the targets accidentally hit, convinced many Afghans that U.S. forces disregarded the lives of civilians.

Nevertheless, on Sept. 16, 2003, Rumsfeld signed an executive order cementing JSOC as the center of the counterterrorism universe. It listed 15 countries and the activities permitted under various scenarios, and it gave the preapprovals required to carry them out.

In Iraq and Afghanistan, lethal action against al-Qaeda was granted without additional approval. In the other countries — among them Algeria, Iran, Malaysia, Mali, Nigeria, Pakistan, the Philippines, Somalia and Syria — JSOC forces needed the tacit approval from the country involved or at least a sign-off from higher up on the American chain of command. In the Philippines, for example, JSOC could undertake psychological operations to confuse or trap al-Qaeda operatives, but it needed approval from the White House for lethal action. To attack targets in Somalia required approval from at least the secretary of defense, while attacks in Pakistan and Syria needed presidential sign-off.

In the fall of 2003, JSOC got a new commander who would turn the organization into arguably the most effective weapon in the U.S. counterterrorism arsenal. From his perch as vice director of operations on the Joint Staff, Brig. Gen. Stanley A. McChrystal had come to believe there was an 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. The new emphasis on interagency cooperation also meant meetings were bigger and longer. Any one of a multitude of agencies could stifle action until it was too late.

McChrystal believed he had “to slip out of the grip” of Washington’s suffocating bureaucracy, he told associates. He moved his headquarters to Balad Air Base, 45 miles northeast of Baghdad, and worked inside an old concrete airplane hangar with three connecting command centers: one to fight al-Qaeda’s affiliate in Iraq, one for the fight against Shiite extremists in the country and a third for himself, so he could oversee all operations.

He coaxed the other intelligence agencies to help him out — the CIA presence grew to 100; the FBI and National Security Agency to a combined 80. He won their loyalty by exposing the guts of his operation to everyone involved. “The more people you shared your problem with, the better you’d do in solving it,” he would say.

McChrystal installed 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.

Then he gave access to it to JSOC’s bureaucratic rivals: the CIA, NSA, FBI and others. He also began salting every national security agency in Washington with his top commandos. In all, he deployed 75 officers to Washington agencies and 100 more around the world. They rotated every four months so none would become disconnected from combat.

Some thought of the liaisons as spies for an organization that was already too important. But those suspicions did little to derail JSOC or McChrystal.

Stories spread that he ate just one meal and ran 10 miles every day. He looked the part, with his taut face, intense eyes and thin physique. A sign inside the wire at Balad said it all: “17 5 2.” Seventeen hours for work, five hours for sleep, two hours for eating and exercise.

McChrystal’s legendary work ethic mixed well with his Scotch Irish exuberance and common-man demeanor. He viewed beer calls with subordinates as an important bonding exercise. He made people call him by his first name. He seemed almost naively trusting. (This trait would become McChrystal’s undoing in 2010, after he was promoted to commander of forces in Afghanistan. He and members of his inner circle made inappropriate comments about their civilian leaders in the presence of a Rolling Stone reporter. McChrystal offered to resign, and Obama quickly accepted).

Harnessing technology

The Iraqi insurgency’s reliance on modern technology also gave tech-savvy JSOC and its partners, particularly the National Security Agency, an advantage. The NSA learned to locate all electronic signals in Iraq. “We just had a field day,” said a senior JSOC commander, speaking on the condition of anonymity to describe secret operations.

One innovation was called the Electronic Divining Rod, a sensor worn by commandos that could detect the location of a particular cellphone. The beeping grew louder as a soldier with the device got closer to the person carrying a targeted phone.

Killing the enemy was the easy part, JSOC commanders said; finding him was the hard part. But thanks to Roy Apseloff, director of the National Media Exploitation Center, the U.S. government’s agency for analyzing documents captured by the military and intelligence community, JSOC’s intelligence collection improved dramatically. Apseloff offered to lend McChrystal his small staff, based in Fairfax, to examine items captured in raids. Apseloff’s team downloaded the contents of thumb drives, cellphones and locked or damaged computers to extract names, phone numbers, messages and images. Then they processed and stored that data, linking it to other information that might help analysts find not just one more bad guy but an entire network of them.

The major challenge was how to find the gems in the trash quickly enough to be useful. The key was more bandwidth, the electronic pipeline that carried information like e-mail and telephone calls around the world. Luckily for the military and JSOC, the attacks of 2001 coincided with an unrelated development: the dot-com bust. It created a glut in commercial satellite capacity, and the military bought up much of it.

Within a year after McChrystal’s arrival, JSOC had linked 65 stations around the world to enable viewers to participate in the twice-daily, 45-minute video teleconferences that he held. By 2006, JSOC had increased its bandwidth capability by 100 times in three years, according to senior leaders.

The other challenge JSOC faced was a human one: Ill-trained interrogators had little information about individual detainees and didn’t know what questions to ask or how to effectively ask them. Worse, some members of the JSOC’s Task Force 121 were beating prisoners.

Even before the Army’s Abu Ghraib prison photos began circulating in 2004, a confidential report warned that some JSOC interrogators were assaulting prisoners and hiding them in secret facilities. JSOC troops also detained mothers, wives and daughters when the men in a house they were looking for were not at home. The report warned these detentions and other massive sweep operations were counterproductive to winning Iraqi support.

Another investigation of JSOC detention facilities in Iraq during a four-month period in 2004 found that interrogators gave some prisoners only bread and water, in one case for 17 days. Other prisoners were locked up 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.

Eventually, 34 JSOC task force soldiers were disciplined in five cases over a one-year period beginning in 2003.

McChrystal ordered his intelligence chief, Michael Flynn, to professionalize the interrogation system. By the summer of 2005, JSOC’s interrogation booths at Balad sat around the corner from the large warren of rooms where specialists mined thumb drives, computers, cellphones, documents to use during interrogations. Paper maps were torn down from the walls and replaced with flat-panel screens and sophisticated computerized maps. Detainees willing to cooperate were taught how to use a mouse to fly around their virtual neighborhoods to help identify potential targets.

JSOC had to use the rules laid out in the Army Field Manual to interrogate detainees. But its interrogators were — and still are — permitted to keep them segregated from other prisoners and to hold them, with the proper approvals from superiors and in some case from Defense Department lawyers, for up to 90 days before they had to be transferred into the regular military prison population.

The new interrogation system also included an FBI and judicial team that collected 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 senior military officials.

Body counts

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 200 of them a month at the high point. By the end of 2005, a shocking picture emerged: Iraq was rife with semiautonomous al-Qaeda networks.

Al-Qaeda had divided Iraq into sections and put a provincial commander in charge of each. These commanders further divided their territory into districts and put someone in charge of each of those, too, according to military officials. There were city leaders within those areas and cells within each city. There were leaders for foreign fighters, for finance and for communications, too.

By the spring of 2006, using the expanded bandwidth and constant surveillance by unmanned aircraft, JSOC executed a series of raids, known as Operation Arcadia, in which it collected and analyzed 662 hours of full-motion video shot over 17 days. The raid netted 92 compact discs and barrels full of documents, leading to another round of raids at 14 locations. Those hits yielded hard drives, thumb drives and a basement stacked with 704 compact discs, including copies of a sophisticated al-Qaeda marketing campaign. Operation Arcadia led, on June 7, 2006, to the death of the al-Qaeda leader in Iraq, Abu Musab al-Zarqawi, when JSOC directed an airstrike that killed him.

JSOC’s lethality was evident in its body counts: In 2008, in Afghanistan alone, JSOC commandos struck 550 targets and killed roughly a thousand people, officials said. In 2009, they executed 464 operations and killed 400 to 500 enemy forces. As Iraq descended into chaos in the summer of 2005, JSOC conducted 300 raids a month. Over 50 percent of JSOC Army Delta Force commandos now have Purple Hearts.

The most intense Iraqi raids reminded McChrystal of Lawrence of Arabia’s description of “rings of sorrow,” the emotional toll casualties take 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.

If killing were all that winning wars was about, the book on JSOC would be written. 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 create huge political setbacks.

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 was only ever about 50 percent, according to two senior commanders. They considered this rate a good one.

“Sometimes our actions were counterproductive,” McChrystal said in an interview. “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.”

In 2008, Bush also briefly sent JSOC into Pakistan. To soothe the worries of U.S. Ambassador Anne Patterson about the mounting civilian deaths from JSOC raids in other countries, commandos brought her a Predator console so she could witness a raid in real time. Because of public outcry in Pakistan, U.S. officials canceled the mission after only three raids. The CIA has continued to conduct drone strikes there.

Targeting bureaucracy

The Defense Department has given JSOC a bigger role in nonmilitary assignments as well, including tracing the flow of money from international banks to finance terrorist networks. It also has become deeply involved in “psychological operations,” which it renamed “military information operations” to sound less intimidating. JSOC routinely sends small teams in civilian clothes to U.S. embassies to help with what it calls media and messaging campaigns.

When Obama came into office, he cottoned to the 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. In 2010, for example, he secretly directed JSOC troops to Yemen to kill the leaders of al-Qaeda in the Arabian Peninsula.

The Arab Spring forced the White House to delay some JSOC missions. In the meantime, the organization is busy with its new 30,000-square-foot office building turned command center. Unlike previous offices, it is not located in some obscure part of the world. It sits across the highway from the Pentagon in pristine suburban splendor, just a five-minute drive from McChrystal’s civilian 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 is not the next terrorist network but another of its lifelong enemies: the Washington bureaucracy. Some 50 battle-hardened JSOC warriors and a handful of other federal intelligence and law enforcement agencies work there.

Mexico is at the top of its wish list. So far the Mexican government, whose constitution limits contact with the U.S. military, is relying on the other federal agencies — the CIA, the Department of Homeland Security, the Drug Enforcement Administration and Immigration and Customs Enforcement — for intelligence collection and other help.

But JSOC’s National Capital task force is not just sitting idly by, waiting to be useful to its southern neighbors. It is creating targeting packages for U.S. domestic agencies that have sought its help, including the U.S. Immigration and Customs Enforcement agency, the second-largest federal law enforcement agency and the latest to make a big play for a larger U.S. counterterrorism role.