One of the greatest ironies of the 9/11 Era: while politicians, generals and journalists lined up to denounce al-Qaida as a brutal band of fanatics, one commander thought its organizational structure was kind of brilliant. He set to work rebuilding an obscure military entity into a lethal, agile, secretive and highly networked command – essentially, the United States' very own al-Qaida. It became the most potent weapon the U.S. has against another terrorist attack.

That was the work of Stanley McChrystal. He is best known as the general who lost his command in Afghanistan after his staff shit-talked the Obama administration to Rolling Stone.

Inescapable as that public profile may be, it doesn't begin to capture the impact he made on the military. McChrystal's fingerprints are all over the Joint Special Operations Command, the elite force that eventually killed Osama bin Laden. As the war on terrorism evolves into a series of global shadow wars, JSOC and its partners – the network McChrystal painstakingly constructed – are the ones who wage it.

These days, McChrystal travels around the country to talk about his leadership style. His insights reveal a lot about how the JSOC became the Obama team's go-to counterterrorism group. "In bitter, bloody fights in both Afghanistan and Iraq," McChrystal has written, "it became clear to me and to many others that to defeat a networked enemy we had to become a network ourselves."

McChrystal's career also reveals a second irony: At the moment of his greatest ascension, to overall command in Afghanistan, McChrystal couldn't take his own advice.

McChrystal declined to speak for this article. He's working on a book, due out in 2012, that will probably shed some light on his tenure at JSOC. This piece is drawn from his speeches, interviews I've conducted over the years with special operations and intelligence veterans – usually off the record – as well as two insightful new books: Counterstrike by Thom Shanker and Eric Schmitt, and Top Secret America by Dana Priest and William Arkin.

McChrystal outlines the terrorist and insurgent networks in Afghanistan.

The Networked Ninja ——————-

The historical problem that special operations forces had, in the eyes of high-level policymakers, is that they weren't ninjas. U.S. commandos trained constantly, but they didn't have much combat experience during the 1980s and '90s.

When the Clinton administration reviewed its options for attacking al-Qaida's Afghanistan safe houses in 1998, President Clinton vented frustration: "You know, it would scare the shit out of al-Qaida if suddenly a bunch of black ninjas rappelled out of helicopters into the middle of their camp."

JSOC certainly knew how to rappel. The problem was it often didn't know where to rappel, or where to send its helicopters, or who the enemy was.

In 2002, a JSOC AC-130 gunship came to relieve a team of commandos who'd come under attack while hunting Taliban leaders in Uruzgan province. The fire it directed against its targets was so heavy that the low estimate of civilian deaths, according to the Afghan government and included in the official U.S. Central Command report on the incident, is 48. Hundreds may have been killed.

JSOC had minimal intelligence capabilities. The CIA, the agency that knew Afghanistan the best and led the hunt for al-Qaida, distrusted it. It was hived off from the conventional military, whose low-level commanders could be left to deal with angry civilians after one of JSOC's raids in Afghanistan or Iraq. McChrystal took command in 2003, began examining al-Qaida, and had something of a revelation.

>'We had to become a network ourselves.'

"[I]t became increasingly clear – often from intercepted communications or the accounts of insurgents we had captured – that our enemy was a constellation of fighters organized not by rank but on the basis of relationships and acquaintances, reputation and fame," McChrystal remembered recently in Foreign Policy. "We realized we had to have the rapid ability to detect nuanced changes, whether the emergence of new personalities and alliances or sudden changes in tactics." Think Bruce Wayne getting inspired by a bat to strike fear into the hearts of criminals.

McChrystal set to work, as he put it, building JSOC's network. One key node: CIA. During a January speech, he recalled how he needed CIA's help getting intelligence on a Taliban leader he was hunting. CIA was secretive, compartmentalized and suspicious of other organizations meddling in its affairs – exactly what JSOC used to be like.

So McChrystal took the rare step of going to CIA headquarters, hat in hand. As it turned out, CIA just needed a promise that JSOC "wouldn't go across the border" into Pakistan, jeopardizing its own operations. McChrystal agreed, the intel flowed, and the Taliban commander was killed.

It was the beginning of a new relationship between JSOC and the vast spy apparatus the U.S. built after 9/11. CIA operatives and analysts would visit McChrystal's base of operations in Balad, Iraq, to plan joint missions.

And not just them: Satellite analysts from the National Geospatial-Intelligence Agency, regional experts from the State Department, and surveillance specialists from the National Security Agency were the next people McChrystal effectively recruited. McChrystal spent his commander's discretionary fund not on better guns, but on purchasing bandwidth so that all the nodes of his network could speak to each other, sometimes during missions.

Veterans of JSOC remember that as crucial. An NSA-created linkup called the Real Time Regional Gateway allowed operatives who seized scraps of intelligence from raids – a terrorist's cellphone contacts, receipts for bomb ingredients, even geolocated terrorist cellphones – to send their crucial data to different nodes across the network. One analyst might not appreciate the significance of a given piece of intel. But once JSOC effectively became an experiment in intel crowdsourcing, it soon got a bigger, deeper picture of the enemy it was fighting – and essentially emulating.

"If you look at JSOC, you're looking at arguably the single most integrated, most truly joint command within the U.S. military," says Andrew Exum, who served in the Army's Ranger Regiment in Iraq and Afghanistan in 2003 and 2004 and who advised McChrystal as a civilian in 2009. McChrystal and his brain trust "were seeking to do and succeeding in doing what many commanders and diplomats and government officials talk about: tearing down the walls that exist between various departments, agencies and military units."

It also helped mitigate JSOC's most horrific mistakes.

Special Operations Forces train. Photo: U.S. Special Operations Command

'No Blood, No Foul,' No More —————————-

Defense Secretary Donald Rumsfeld gave JSOC the authority to hold prisoners for 90 days before transferring them to military detention facilities. That gave JSOC jailers nearly limitless authority over their captives. Unsurprisingly, some began abusing it, beating prisoners senseless in a facility called Camp Nama – which Saddam Hussein used as a torture chamber – where the slogan was, "No Blood, No Foul."

Although no public investigation has ever been conducted into the abuses at Nama, McChrystal reportedly said "This is how we lose," when he toured the facility for the first time. He assigned his top intelligence officer, then-Brig. Gen. Michael Flynn, to professionalize JSOC interrogations. Flynn reached out to trained interrogators throughout the U.S. bureaucracy and even to around the world to provide instruction.

Subsequent interrogations of suspected al-Qaida captives in Iraq relied on Saudis brought in when a Saudi national was nabbed, Egyptians when an Egyptian was. Priest and Arkin report that detainees would even be videoconferenced in with their families – who'd plead with their sons to cooperate.

>'This is how we lose.'

Think about that for a minute. JSOC is the most secretive organization in the U.S. military. Its detention and interrogation operations are among its most sensitive missions. And the family members of terrorist suspects actually got a glimpse inside them, all as a method of building rapport.

Not only that, diplomats, NSA techs, intelligence analysts of all stripes, and foreign government officials became – effectively – JSOC adjuncts, so JSOC could leverage their expertise. Despite years of post-9/11 lip service to breaking down bureaucratic barriers, JSOC actually did it, for the most important and secretive operations the military undertook.

Flynn was arguably McChrystal's most important partner in building JSOC's network. "We once had a problem in terms of how we were going to track our units on the ground using satellite technology. It's almost unthinkable today because of GPS, Blue Force Tracker and so forth," recalls Andrew Exum, now a senior fellow at the Center for a New American Security, referring to a GPS receiver system that allows U.S. troops to track the movements of their allies. "I remember Gen. Flynn's solution was to track down a really smart engineer at Georgia Tech University, who developed a piece of software for use by commercial aircraft. It went outside the standard Army acquisition process – we'd still be waiting for the equivalent of Navstar if [Flynn] hadn't. But the fact that he was comfortable interacting in the world outside of the military in order to achieve an effect says a lot about him."

McChrystal left JSOC in early 2008 to take a senior position working for Adm. Mike Mullen, the Chairman of the Joint Chiefs of Staff. The network he built was getting results. In June 2006, JSOC killed al-Qaida's leader in Iraq, Abu Musab al-Zarqawi. (McChrystal had Zarqawi's corpse brought to his office for personal inspection.)

During the Iraq surge, JSOC raided suspected terrorist safe houses on a nightly basis, something McChrystal's friend David Petraeus would repeat in Afghanistan. McChrystal left JSOC in the hands of his friend and deputy, Vice Adm. William McRaven – and the conclusion from President George W. Bush was, "JSOC is awesome."

But McChrystal would never enjoy the same success again.

A boy watches McChrystal observe a meeting in Afghanistan's Kandahar Province. Photo: ISAF

The Un-Networked McChrystal —————————

Defense Secretary Robert Gates tapped McChrystal to lead the Afghanistan war in May 2009. JSOC veterans were thrilled. "The man is unstoppable," wrote one, using the pseudonym Dalton Fury. "McChrystal has few peers and makes even fewer mistakes." He was about to make a lot of them.

The McChrystal of JSOC enlisted people from across the bureaucracy into his network. That turned out to be much easier to do when running an organization of only a few thousand people. Securing the buy-in of a multinational military coalition comprising 140,000 was far more challenging.

McChrystal had early successes coaxing Afghan President Hamid Karzai, who resented the Obama administration's arms-length relationship. "His approach to President Karzai was humility," recalls Exum, who advised McChrystal that summer. "He had the attitude of, 'I'm here to support you, the Afghan president.'"

Some in uniform weren't so sure they enjoyed their commander's support. McChrystal faced the unenviable task of curbing NATO's accidental civilian deaths – he called Afghan public opinion "strategically decisive" – while beating back an inflamed Taliban insurgency.

Two of his earliest moves to that end inadvertently made his troops question his support. One was his August counterinsurgency guidance, which instructed troops to show outright deference to Afghans, down to giving them right of way on the roads. The other was his Tactical Directive, which sharply restricted the rules of engagement for combat aircraft, something that alarmed troops who feared a loss of crucial air support.

>'I would love to kick McChrystal in the nuts.'

Both of those decisions were made for defensible reasons. Losing the support of Afghanistan's people was more destructive to the war than losing any firefight to the Taliban. But McChrystal didn't sufficiently sell his decisions to his own troops, explaining to them why they were ultimately in their interests.

"I would love to kick McChrystal in the nuts," a Special Forces veteran told Michael Hastings for his fateful McChrystal profile in Rolling Stone. "His rules of engagement put soldiers' lives in even greater danger."

There was something else missing from McChrystal's network: the U.S. embassy in Kabul. While McChrystal and Ambassador Karl Eikenberry, a former Afghanistan war commander himself, supposedly enjoyed good relations, the embassy and NATO sometimes seemed like they weren't in the same country.

Then one of Eikenberry's cables back to Washington casting doubt on McChrystal's desired troop surge leaked to the press. That poisoned the well. "Here's one that covers his flank for the history books," McChrystal kvetched to Hastings. "Now if we fail, they can say, 'I told you so.'"

But the surge itself was causing a breach with the most important node in McChrystal's network: the White House. In the 2009 debates over sending more troops to Afghanistan, President Obama reportedly felt like the military was boxing him into an unwise escalation.

McChrystal, in London for one of his first public appearances, bluntly remarked that he thought all other strategies were doomed. Although McChrystal repeatedly defended the Obama team, the press went wild with a narrative about an insubordinate commander, and not without some justification. Obama ultimately endorsed the surge, but it was, at best, a Pyrrhic victory for McChrystal.

Nor were McChrystal's battlefield moves showing the same success that JSOC had demonstrated. Through the summer and fall of 2009, Marines fought furiously through Helmand Province, for little obvious gain. That February, he and Karzai invaded the Helmand town of Marja, proclaiming that he had a "government in a box" ready to establish order in the cleared town. Instead, fighting continued for months, without a significant Afghan government presence.

All that meant that McChrystal, the consummate networker, was out of allies when Hastings quoted McChrystal's aides making derogatory comments about the Obama team. Quick to defend his loyal staff and take responsibility, McChrystal immediately offered to resign.

Obama took him up on it. A sterling career was unexpectedly over.

People close to McChrystal were mystified by the uncharacteristic self-marginalization. "In every review of COIN [counterinsurgency] best practices, 'unity of effort' tops the list," one of his advisers told Danger Room last year. "Every. Single. Review. And we're totally fucking it up; fucking up the one thing that should be in our control." The McChrystal of JSOC never needed to be reminded.

McChrystal meets with President Obama in Copenhagen. Photo: ISAF

The Network Strikes Back ————————

McChrystal and Obama have patched things up. Obama tapped McChrystal to spearhead a White House effort to support veterans' families. McChrystal has never expressed public bitterness about losing his command, and even joked about his mistakes during his July 2010 retirement.

Some close to McChrystal say that what hurt him the most is that he had to leave Afghanistan before he could implement a turnaround in U.S. fortunes. When his friend Petraeus took over the war, Petraeus reversed McChrystal's restrictions on air power, leading to the biggest aerial bombardment in the war thus far.

Petraeus also relied on McChrystal's protege McRaven at JSOC for a relentless pace of raids on Taliban forces. Only by the time Petraeus relinquished command in July, the war – in the view of the CIA, among others – was stalemated.

>'JSOC is the single most truly joint command within the U.S. military.'

But JSOC had just experienced its finest hour – the fulfillment of the ultimate goal of McChrystal's networking strategy. A Navy SEAL team killed Osama bin Laden. The mission was planned by McRaven, ultimately quarterbacked by CIA Director Leon Panetta, and relied extensively on both CIA analysis and JSOC's years of raiding in Afghanistan.

What was bureaucratically unthinkable before McChrystal is now routine: JSOC and CIA, matched with other government elements, now hunt al-Qaida worldwide in expanding, secretive wars.

Nor is that likely to change. McChrystal's allies and proteges are all over the security bureaucracy. McRaven now runs all U.S. Special Operations Forces. Petraeus now runs the CIA. McChrystal's fellow Army Ranger, Lt. Gen. Joseph Votel, now runs JSOC. Flynn is the assistant director of national intelligence. Ten years after 9/11, al-Qaida's network looks more brittle than ever, while JSOC's is robust.

The network McChrystal built, McRaven enhanced and Votel inherits comes in stark contrast to the rest of the U.S. security bureaucracy, which Priest and Arkin call "Top Secret America" and which remains disconnected, bloated and expensive. Priest and Arkin bluntly conclude that McChrystal turned JSOC around "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."

What the post-9/11 reforms failed to accomplish across the sprawling national security apparatus, McChrystal did in miniature.

"We had to figure out a way to retain our traditional capabilities of professionalism, technology, and, when needed, overwhelming force," McChrystal recalled in Foreign Policy, "while achieving levels of knowledge, speed, precision, and unity of effort that only a network could provide."

It didn't work in Afghanistan with conventional forces. But now it's up to the secretive, lethal network that McChrystal established to finally destroy the terrorist network that inspired it.

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