Soldiers with the 20th Special Forces Group walk a flight line during 2014 Emerald Warrior exercises

Soldiers with the 20th Special Forces Group walk a flight line during 2014 Emerald Warrior exercises DoD photo by Senior Airman Jodi Martinez, U.S. Air Force

Inside America's Shadow War on Terror—and Why It Will Never End

As the Afghanistan war winds down, the war against extremists is nowhere near finished. By James Kitfield

The muezzin's call to predawn prayers had not yet woken the seaside Somali town of Barawe when a lone figure stepped out of a two-story villa near the water's edge. In the darkness of a walled compound, he smoked a cigarette, the glow of ash rhythmically illuminating his face. It was an effect that was heightened by the night-vision goggles focused on him. When the man stepped back inside, the commander of Navy SEAL Team Six, his own face hidden under black grease, directed his commandos to take up their positions and storm the villa. The date was Oct. 5, 2013, and inside was a Kenyan named Abdikadir Mohamed Abdikadir, or Ikrimah—the leader of al-Shabaab suspected of masterminding the gruesome killing of non-Muslims at Nairobi's Westgate Mall.

Two hours later and nearly 3,000 miles away, a Libyan named Nazih Abdul-Hamad al-Ruqai, or Anas al-Libi, was returning from dawn prayers as the sun began to rise over Tripoli. His sedan pulled up to a comfortable house in an upscale suburb of the capital and was suddenly boxed in from the side and the front by two white vans with darkened windows. Commandos from the Army's elite Delta Force counterterrorism unit leaped out, one training his gun on al-Libi from the front as another broke the window, pulling the terrorism suspect out of the car and bundling him into one of the vans before both vehicles and a third that had been hidden sped off. The entire operation, caught on a surveillance camera and posted on YouTube, took 60 seconds.

President Obama wants deeply to convince Americans that the time of perpetual war is over. "America is at a crossroads," he said last year in a speech that was meant to reassure a weary public that the post-Sept. 11 era of invasion, regime change, and nation-building was nearly done. "Beyond Afghanistan, we must define our effort not as a boundless 'global war on terror,' but rather as a series of persistent, targeted efforts to dismantle specific networks of violent extremists that threaten America."

Yet these twin raids, executed just hours apart in different time zones and inside countries with which the United States is not at war, demonstrate that the conflict is far from over. The unique U.S. counterterrorism model of intelligence-driven operations by multiagency task forces around the globe represents war—perhaps by another name, but deadly and perpetual, nonetheless.

Indeed, even after the last U.S. combat troops leave Afghanistan this year, the shadow war against jihadi terrorists that began on Sept. 11, 2001, will rage on, executed by comingled military, intelligence, and law-enforcement capabilities using legal authorities that blur distinctions between uncommon criminals and enemy combatants. Terrorism suspects caught in the hard stare of the U.S. counterterrorism network will still be arrested by U.S. law-enforcement agents overseas; snatched off the streets of lawless cities by U.S. special operations forces; eviscerated by CIA drone strikes in remote areas far from any declared war zone; and interrogated under the rules of warfare before being read their Miranda rights and prosecuted in federal courts. And that life-and-death struggle will continue to play out largely in secret.

National Journal was offered a glimpse behind that curtain of secrecy, visiting with U.S. counterterrorism warriors who have been on the front lines of this fight for many years. Their war did not end when Osama bin Laden's body slipped off the deck of a U.S. warship in 2011, nor will the enemy surrender when the last airman turns off the lights at Bagram Air Base in Afghanistan. Rather, theirs is a twilight struggle in which ancient hatreds are kindled anew and show no sign of resolution.


Like many top national security and counterterrorism officials today, Lt. Gen. Michael Flynn honed his craft as a field-grade officer in the crucible of war. As the former intelligence chief for Joint Special Operations Command in Iraq and Afghanistan, Flynn helped his boss and mentor, former JSOC Commander and now-retired Army Gen. Stanley McChrystal, develop the model of intelligence-driven, targeted strikes that has largely come to define U.S. counterterrorism operations: find, fix, finish, exploit, and analyze (or "F3EA" in militaryspeak).

Today, the rhythms of that cycle ripple through the vast U.S. counterterrorism network: meticulous intelligence-gathering to establish "patterns of life" for terrorism targets; followed by raids and arrests (or, in extreme cases, lethal strikes); then interrogations, and exploitation of evidence such as computer hard drives or smartphones; and follow-up analysis leading to further raids or arrests. This is repeated in a loop that continually strengthens linkages in the U.S. counterterrorism network and expands intelligence databases, all while degrading the enemy.

It's an intelligence system that has yielded an alarming picture of the new terrorist enemy. Yes, the al-Qaida that attacked the United States on 9/11 has been devastated by a decade of drone strikes and arrests in Pakistan. But Qaida affiliates and sympathetic Islamic extremist groups have proliferated to fill that void, especially in the revolution-riled Middle East and Africa.

That loose and still gravely dangerous network includes al-Qaida in the Arabian Peninsula, known as AQAP, which has launched three attacks on the United States from its base in Yemen and was targeted in a series of U.S. drone strikes in April that killed more than 40 of its suspected members. Al-Qaida in the Islamic Maghreb, or AQIM, expanded from its base in Algeria last year to capture much of northern Mali before being pushed back by U.S.-supported French and African forces. Al-Shabaab, the Qaida affiliate in Somalia responsible for last year's massacre in the Kenyan shopping mall that killed 67 civilians, sits near the top of the most-dangerous list, as does Boko Haram, the Islamic extremist group behind the grisly massacres of non-Muslims in Nigeria and the recent kidnapping of more than 200 schoolgirls, and Ansar al-Sharia, a radical group in Libya tied to the 2012 murder of U.S. Ambassador Chris Stevens and three other Americans. As if that were not enough, a viper's nest of Qaida- and Taliban-linked Islamic extremist groups remains active in Pakistan and Afghanistan.

Most worrisome to Flynn and other U.S. counterterrorism experts is the situation in Syria, where a prolonged civil war is beginning to resemble the conflict in Afghanistan in the 1980s and 1990s that originally spawned al-Qaida and the Taliban. The recently renamed Islamic State of Iraq and Syria (formerly al-Qaida in Iraq), and the Qaida-affiliated al-Nusra Front have attracted more than 7,000 foreign fighters to their black banners in Syria, hundreds of them from Europe and the United States; the groups control territory and enjoy a degree of sanctuary stretching from northern Syria to Anbar province in western Iraq. U.S. counterterrorism officials are mindful that Arab fighters such as bin Laden, who joined the Afghan mujahedeen in fighting the Soviets in the 1980s, brought the campaign of terror home with them, before exporting it globally.

This decentralization and proliferation of the Qaida threat drove a 43 percent increase in worldwide terrorist attacks between 2012 and 2013, according to the State Department's recently released global terrorism report. "I actually think al-Qaida is becoming more dangerous as it decentralizes, and through its franchises it has a bigger footprint today than on September 11, 2001," says Flynn, now director of the Defense Intelligence Agency.

As the intelligence chief for JSOC in both Iraq and Afghanistan, Flynn helped capture many local leaders of al-Qaida and the Taliban. Many of those hardened militant field commanders have since either been released, in the case of Afghanistan, or freed in a series of bold prison breaks in Iraq. In both cases, Flynn notes, they've returned to the battlefield. "They have gotten smarter from applying the lessons learned from fighting us, in many cases they are better armed and funded than in the past, and they are more sophisticated in knowing how to target and control weak governments and societies in the Muslim world through fear and intimidation." He notes that leaders of al-Qaida's far-flung network of affiliates and associated jihadists still communicate regularly with core Qaida leader Ayman al-Zawahiri, thought to be hiding in Pakistan's tribal regions, as well as with each other.

If Zawahiri were ever able to unite them under a single banner and strategy, today's al-Qaida would be tantalizingly close to bin Laden's vision of a global Islamic insurgency intent on waging endless war, locally, regionally, and against the West. "If the growing number of al-Qaida affiliates become more coherent and cohesive as a group, then we will have a very big problem on our hands," Flynn warns. "They are not there yet. But knowing what I do about this enemy and its evolution over the last 10 years, as I look forward to the next 10 or 20 years, I see this threat being with us for a very, very long time."


Only months after Obama's counterterrorism speech at National Defense University last year, the contours of the secret war against Islamic extremists came briefly into view with a series of events compressed into a few short weeks yet spread out over thousands of miles and across multiple international borders, none of them near Afghanistan.

The unlikely series of events began at the sprawling Westgate Mall in Nairobi, a retail oasis of upscale shops and restaurants favored by wealthy Kenyans and tourists, including plenty of Americans who were among the crowd strolling through the mall looking for souvenirs on Sept. 21, 2013.

Initially, few people took note of the silver Japanese compact car that pulled into a restricted zone next to the mall and parked illegally. Four young men piled out with their heads swathed in the signature black head scarves of the Somali Shabaab terrorist group, and once inside the building they calmly shouldered assault rifles. After shouting for any Muslims to raise their hands and exit the mall in Christian-majority Kenya, the assailants began methodically shooting into the terrified crowd.

By the end of the second day of the siege, scores of victims lay in a makeshift morgue outside the mall, part of a body count that would grow to nearly 70 civilians, many of them young children. Four Americans were among the nearly 200 people wounded in the attack. Already, an FBI Rapid Deployment "Fly Team" was on the scene. Special Agent in Charge Richard Frankel stood behind a barricade outside the wreckage of Westgate, listening to sporadic gunfire and waiting for the signal to send in his team of more than 80 investigators.

The tactical command post set up on the perimeter of Westgate mirrored the multi- agency Joint Terrorism Task Forces that are spread across the United States. The Kenyan task force was crawling with agents and operators from the major U.S. intelligence, law-enforcement, and military agencies, many of them familiar faces and veterans of JSOC's task forces in Iraq and Afghanistan.

The job of Frankel's FBI team was to conduct "sensitive site exploitation." His investigators helped to interview eyewitnesses, process the car for fingerprints, review videotape from the surveillance cameras, and conduct a methodical search of what was left of the still-smoldering mall. FBI forensics experts categorized each piece of evidence, from shell casings to cell phones, noting exactly where it was found and whom it was most likely connected to. By matching surveillance videos with evidence on the ground, they determined where the shooters killed certain victims and, most important, where they bedded down inside the mall that first night. That was where FBI forensic experts found a trove of evidence.

Before long, Frankel's team knew that the media reports of a dozen or more Shabaab fighters were way off mark. They were tracking four shooters and perhaps a fifth facilitator. "Our primary mission at that point was to help the Kenyans identify the terrorists who were responsible for the massacre, and hopefully gather enough evidence to track and ultimately prosecute them," Frankel says.

The presence of such FBI Fly Teams at the scene of major terrorist attacks worldwide speaks to the bureau's post-9/11 transformation from primarily a law-enforcement agency into a critical counterterrorism player, a process also heavily informed by the lessons of Iraq and Afghanistan. A turning point came in 2006, when the U.S. Embassy in Kabul was hit by a suicide bomber who killed two American soldiers and 14 Afghan civilians.

Brian McCauley was the FBI legal attaché in the embassy at the time. After witnessing the attack, he was alarmed to see Afghan police and NATO forces rush to the scene and wash down the gory bomb site with hoses, destroying vital forensic evidence in the process. At McCauley's request, FBI headquarters in Washington deployed more than 100 special agents to Afghanistan, where they launched a conspiracy investigation aimed at the terrorist cells in Kabul that were targeting U.S. and allied troops with suicide bombers and improvised explosive devices. Working with JSOC, the FBI investigation eventually identified more than 150 IED "facilitators" whom special operations forces either captured or killed, foiling 43 bombing plots in the process.

Those hard-earned lessons inform the FBI's close coordination with JSOC and the full panoply of U.S. counterterrorism forces. "We all learned in Afghanistan that no single agency can win this fight by themselves, but working together, we had a lot of success in disrupting these terrorist networks and cells," says McCauley, now the deputy assistant director of the FBI's International Operations Division.

Today, with only hours of notice and a green light from the chain of command, U.S. counterterrorism forces can rapidly deploy a major new node in a globe-spanning intelligence network that includes hundreds of thousands of investigators, intelligence analysts, military operators, and private contractors stationed in more than 160 countries. That model of multiagency cooperation and intelligence-driven, targeted operations has expanded well beyond Afghanistan, McCauley notes. "We've now learned to align our threat assessments, and the place where we all see the terrorist threat migrating and growing is Africa. So we need to respond to that before some weakly governed place in Africa becomes the next terrorist sanctuary, like Afghanistan was in the 1990s."

Around the time of the embassy bombing in Kabul, the Drug Enforcement Administration also began working closely with JSOC to track Afghan drug kingpins whose proceeds were helping to fuel the Taliban insurgency. To participate jointly in JSOC raids, in 2006 DEA created Foreign Advisory Support Teams, units whose commandos undergo training that rivals the military special forces they often work alongside. In one case that DEA investigated, an Afghan drug cartel was trafficking methamphetamine to California and using the proceeds to fund the same suicide bomber cells in Kabul that the FBI was tracking. "So working with JSOC in Afghanistan took the blinders off for everyone, and taught us that we were facing a common threat," says Derek Maltz, director of DEA's Special Operations Division. "And the best way to attack that kind of complex organization is not only to go after its leaders, but to also attack its money trail, its logistics infrastructure, and its arms smuggling."


The FBI Fly Team's raw information on the militants likely behind the Westgate Mall attack, like all foreign and domestic intelligence on the terrorist threat, was relayed in real time to the round-the-clock operations center of the National Counterterrorism Center in Washington's Virginia suburbs, near Tysons Corner. The Liberty Crossing campus that houses both the NCTC and the Office of the Director of National Intelligence—two institutions that did not exist before 9/11—stands at the pinnacle of a far-flung empire of "fusion centers" that have proliferated over the past decade, and it acts as the central nervous system of the United States' global counterterrorism network.

Each day inside Liberty One, a nondescript, modern edifice of gray stone that is one of the most-wired buildings in the world, hundreds of counterterrorism experts from more than 20 intelligence, national security, and law-enforcement agencies sift through thousands of reports of raw, terrorism-related intelligence from more than 100 databases. Each threat is cross-checked against the NCTC's own Terrorism Identification Datamark Environment watch list of more than 740,000 suspected or potential terrorists, and analysts choose the top 30 or 40 most credible threats to post to the NCTC's threat matrix. Through an analytic process that is as much art as science, analysts then prioritize a handful of the most urgent threats and flag them in the classified Situation Report that the NCTC publishes for the top levels of government twice a day. Those high-priority threats dominate discussion during the three video teleconferences the intelligence community holds each day, and are also included in the Presidential Daily Briefing delivered at the White House each morning. 

Terrorism threats that make it into the Situation Report and the Presidential Daily Briefing are generally assigned to special NCTC "pursuit groups" consisting of analysts from multiple agencies whose sole task is to find the connections in the digital intelligence clutter—to discover that this email or that phone number links two individuals and sets off an alarm. Established after the NCTC failed to discern the terrorist plot of the so-called underwear bomber, Umar Farouk Abdulmutallab, on Christmas Day 2009, the pursuit groups are the hunters at the top of the intelligence food chain, taking the art of finding patterns of life of potential targets to the next level.

That constant process of filtering and prioritizing terrorist threats from all-sources intelligence requires extraordinary resources and manpower, but NCTC Director Matthew Olsen believes it realizes the 9/11 commission's vision of a single clearinghouse that allows analysts to connect the dots on most terrorist plots. "In the beginning of the NCTC, that was probably more vision than reality, but now in our 10th year I do think we've achieved the goal of being the one place where all the most sensitive information on terrorism comes together and is visible to all the major stakeholders," Olsen said in an interview. "I can tell you our products on specific terrorist-threat streams are regularly disseminated across the government, including to the White House."

As it turned out, two major streams of intelligence intersected at the top of the NCTC's threat matrix last October: one from al-Shabaab's Westgate Mall attack and the other involving longtime Qaida operative al-Libi, the man under indictment for his role in the 1998 bombing of the U.S. embassies in Kenya and Tanzania. On the radar of U.S. intelligence agencies for more than a decade, al-Libi had recently been spotted in his hometown of Tripoli. More important, there was intelligence indicating that core Qaida leaders in Pakistan had sent al-Libi home to establish a new cell in the chaotic landscape of Libya post-Muammar el-Qaddafi, a weakly governed country ruled by competing militias where Ambassador Stevens and three other Americans had been killed by Islamic militants in Benghazi the year before.

In the kind of planning process that once would have taken months, the Obama administration quickly made the decision to launch two nearly simultaneous operations thousands of miles apart, involving the U.S. military's two elite counterterrorism strike forces—Navy SEAL Team Six and the Army's Delta Force. Paradoxically, on Oct. 5, the date chosen for the commando raids, the rest of the U.S. government was shut down by political paralysis in Washington.


The SEAL team in Somalia was given the order to storm the seaside villa. But, according to numerous media reports that included eyewitness accounts, the Shabaab fighter who had retreated inside came back out, firing an AK-47 before SEAL Team Six could reposition. The U.S. commandos fought their way into the villa, but encountered heavy fire and saw more women and children than expected, scrambling for cover. Having lost the critical element of surprise, the SEAL commander ordered his team to retreat to inflatable boats waiting on the beach.

The team could take solace that they suffered no casualties and had sent a message to Shabaab leaders about the long reach of U.S. counterterrorism forces. That message was underscored a few days later when, outside another Somali town, a car carrying two top Shabaab commanders, including the group's chief bomb-maker, was destroyed by a Hellfire missile. The armed Predator drone that fired the missile was most likely operated by the JSOC team attached to the U.S. Africa Command's Combined Joint Task Force–Horn of Africa, headquartered in nearby Djibouti.

After being snatched from the street in front of his family's home, al-Libi was below decks in a spare interrogation room aboard the USS San Antonio. An FBI agent was there too, reading al-Libi his Miranda rights. The suspect now had the right to remain silent, and anything the Libyan said would certainly be used against him in a court of law. If he could not afford an attorney, one would be provided. Anointed with those magic words, the man was suddenly transformed from an "enemy combatant" in America's war with al-Qaida to just another terrorism suspect in the U.S. justice system.

The FBI special agent sitting with al-Libi was part of the government's High-Value Detainee Interrogation Group, another multiagency hybrid peopled by senior military, intelligence, and law-enforcement officials and created specifically for the war against al-Qaida. Because the warship was in international waters somewhere in the Atlantic, and they were operating under broad wartime authorities bestowed by Congress in the post-9/11 Authorization for the Use of Military Force, the spies and the soldiers could question al-Libi indefinitely. They no longer used long-since banned "enhanced interrogation techniques," and what they learned could not be used in a court of law. But they could keep at it with patience and maddening persistence and a psychological jujitsu that appealed to the terrorist's sense of self-importance.

At first al-Libi cooperated with the interrogators, and even after being read his rights, he waived them for a time. But he was ill, and as he tired under the questioning, his mood soured until he invoked Miranda and stopped talking. At that point, the interrogation team halted the questioning and made arrangements to have al-Libi flown to New York City. Within days, the gray-bearded terrorism suspect was standing before a judge in a federal District Court in New York, pleading not guilty and requesting a court-appointed attorney.

All of these operations—from the twin raids and the Predator strike to the Westgate investigation and al-Libi's floating interrogation—demonstrate the global nature of this ceaseless war. It's why the Pentagon continues to add special operations forces (from 61,000 in 2012 to nearly 70,000 by 2015, representing a 300 percent increase compared with pre-9/11 levels) and to increase the size of the unmanned drone arsenal by more than 30 percent even as it reduces ground forces to field the smallest Army since before World War II. It's why the U.S. intelligence budget has more than doubled since 9/11 to more than $75 billion annually, and why the number of FBI Joint Terrorism Task Forces has grown from 26 to more than 100.

"It takes a network to defeat a network," McChrystal has often said.

"In the beginning, it was difficult even putting all these different agencies under one tent with our Joint Task Forces, and suspicions ran so high that I remember one agency putting crime-scene tape around its work stations," the former JSOC commander told National Journal in an interview last year. Over time, success built greater interagency trust. "And as we built the network, we were able to hit the enemy faster and with an operations tempo that was really crushing to them, because they keep losing experienced leaders. That's our counterterrorism model and the heart of our strategy," McChrystal said. "We became like an industrial machine—the of counterterrorism."

Indeed, the 16 major agencies in the intelligence community have institutionalized a wartime ethos of information-sharing and intelligence-focused operations to create a frighteningly efficient counterterrorism model. DIA's Flynn and his cohorts atop peer agencies, including Director of National Intelligence James Clapper, are determined that the synergy is not lost as the post-9/11 wars wind down and bureaucracies in Washington begin to assert themselves anew. For them, there is no end in sight to this war, as their ongoing activities attest.

The White House clearly wants the nation to rediscover its peacetime equanimity. Yet the president has publicly defended the continued use of lethal drone strikes even against American terrorism suspects, as well as snatch-and-capture operations by special operations forces on foreign soil and the NSA's warrantless monitoring of the communications of non-U.S. citizens. And his call for an eventual repeal of wartime authorities feels more aspirational than real. Obama gets the Presidential Daily Briefing, he's seen the threat matrix, and he sat in the loneliest chair in the White House as SEAL Team Six followed his orders to the faraway compound of Osama bin Laden. He's seen the wisdom in Winston Churchill's words that we sleep safely at night because rough men (and women) stand ready to visit violence on those who would do us harm.

So, despite an insistence that things will change after Afghanistan, the counterterrorism model born there will live on to fight a war that is not going away.