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Macmillan Childrens Publishing Group


The Untold Story of America's Secret Campaign Against Al Qaeda

Eric Schmitt and Thom Shanker

Times Books




At the U.S. Embassy in Kuwait City, Brigadier General Jeffrey Schloesser watched in horror—but not surprise—the sickening images from 6,500 miles away that flickered from the television screen. It was Tuesday afternoon, September 11, 2001.

Schloesser, a forty-seven-year-old former Army Special Operations helicopter pilot from Kansas, was one of a small number of counterterrorism experts in the military's ranks. He spoke fluent Arabic and was steeped in Middle East politics and history, having earned a master's degree from Georgetown University's School of Foreign Service and served a yearlong tour in Jordan. He was now serving as the embassy's liaison to the Kuwaiti military.

For Schloesser and for many of his uniformed and civilian colleagues serving in the Middle East, the United States had been in an undeclared war with Al Qaeda long before this day. Eleven months earlier, on October 12, 2000, Al Qaeda operatives in a small skiff had detonated a one-thousand-pound suicide bomb alongside the Navy destroyer USS Cole as it refueled in the port of Aden, on Yemen's southern coast. Seventeen American sailors were killed, and thirty-nine others injured in the blast that ripped a forty-by-forty-foot blackened gash in the ship's port side. The gloves are coming off now, Schloesser had thought then. But the deadly strike failed to outrage the American public.

After the Cole bombing, the movements and travel of American embassy employees and their families in Kuwait were sharply restricted. Al Qaeda had failed in an eerily similar but less publicized attack against the Navy destroyer USS The Sullivans earlier that January as part of the 2000 millennium plots. The terrorists' plan had been to load a boat full of explosives and blow it up near the warship during a port call in Yemen. But the plotters overloaded the skiff, causing it to sink to the bottom of Aden harbor. Months later, after leaving Kuwait, Schloesser would learn that an Al Qaeda operative had been captured carrying a chilling set of blueprints, plans of the house next door to where he and his wife, Patty, had lived. Years later, it gave Patty Schloesser the creeps just thinking about it.

Now, as the searing Kuwaiti summer afternoon gave way to a hazy evening, Schloesser and the CIA station chief looked away from the television images and locked glances with their boss, Ambassador James A. Larocco, a career foreign service officer who had served tours in Egypt, Israel, and Saudi Arabia. "Guys, we've got to take immediate steps right here," Larocco said. As the three men rushed out of the station chief's office to report to superiors in Washington, coordinate with Kuwaiti security forces going on alert, and check in with a spider web of informants and spies for clues to a possible next wave of attacks, each man felt it in his gut: Al Qaeda. For Schloesser, who was already preparing to leave for a new assignment at the Pentagon, a decade of planning and carrying out a secretive counterterrorism campaign against Al Qaeda was just beginning.

* * *

Juan Zarate stood at the window of his new fourth-floor office at the Treasury Department in Washington looking south toward the Pentagon. Clouds of billowing black smoke smeared the early morning sky. "Jim, I can tell you right now, the Pentagon's been hit!" Zarate yelled over the phone to his former boss at the Justice Department, James S. Reynolds, whom he had called to alert to the strikes. "We're under attack!"

Three weeks earlier, Zarate had been a rising star in the Justice Department's terrorism and violent crimes section. With degrees from Harvard College and Harvard Law School, Zarate had been a young federal prosecutor assisting on some of the biggest cases in the burgeoning field of counterterrorism.

The son of immigrants—his mother from Cuba; his father, a physician, from Mexico—Zarate had already lived a life that was a classic all-American success story. Raised in Orange County, California, in a politically conservative family, he showed an interest in security conflicts at a precocious age. As a fifth grader, he wrote a term paper on the war in Angola in the 1970s and the role of Cuban forces there. Zarate, balding, with rimless glasses, looked older than his thirty years. As a junior-level attorney, he had already participated in the prosecutions of the bombers of the U.S. embassies in Kenya and Tanzania in August 1998, attacks organized by Al Qaeda that killed 224 people and wounded thousands. Later, his superiors assigned him to cases involving Hamas, the FARC insurgent group in Colombia, and the attack on the USS Cole. The Cole bombing, in particular, was seared in his mind after he pored over the graphic photos of damage to the ship and the sailors killed on board. "If the American people saw what we're seeing, they'd demand war," Zarate said.

When the Treasury Department came calling in August 2001 and offered to make him part of a senior team running its international financial enforcement and sanctions branch, Zarate jumped at the chance to broaden his counterterrorism credentials and delve into the murky world of illicit financing. Three weeks later, on September 11, Zarate could barely find his new office in the cavernous Treasury Department building, much less know which levers to pull and which people to call in a crisis. It left him feeling momentarily helpless. "If I were back at DOJ, I'd know what to do, who to call," he said. "I didn't really know what to do here yet." Zarate followed his instincts, which were screaming, "Al Qaeda, Al Qaeda," and called his former colleagues at Justice to offer his assistance.

As a Californian, Zarate was quick to remind federal investigators to watch for aircraft flying from the West Coast, not just the East Coast. Zarate had a flashback to an earlier failed Al Qaeda plan: the so-called Bojinka plot, hatched in the Philippines in 1995, to bomb twelve American commercial jets as they flew over the Pacific. That scheme unraveled only after extensive planning and even some trial runs. One of the conspirators in that plot was a man named Khalid Shaikh Mohammed, whom authorities would later identify as the mastermind of the September 11 attacks. "Bojinka animated a lot of our thinking," Zarate said. "We expected more attacks. We anticipated more attacks. The only question in my mind was size and scope."

Soon after the strike on the Pentagon, Zarate and a handful of senior Treasury officials rushed from their offices to the Secret Service headquarters six blocks away, where they watched the day's events unfold from the service's command center. Within months, Zarate would become the point man for the Treasury—and for much of the U.S. government—tracking the movement of money through the murky channels of terrorist financing, dissecting the sophisticated and shadowy networks of donors, illicit activities, and other sources that filled terrorist and insurgent coffers. From Justice to Treasury and ultimately to the upper echelons of the White House's National Security Council, Zarate would over the next decade employ his keen intellect, near-photographic memory, and deft ability to bring together disparate players in the government's bruising internal bureaucratic battles over how to carry out the Bush administration's global war on terror.

* * *

On the morning of September 11, Michael G. Vickers was immersed in the details of plans to help transform the Pentagon by creating lighter, faster, and more lethal forces to deal with emerging threats. Vickers directed strategic studies at the Center for Strategic and Budgetary Assessments, one of the leading independent defense research organizations in Washington. Restructuring the armed forces was one of the Pentagon's top priorities in the early days of the Bush administration. Defense Secretary Donald H. Rumsfeld was in the midst of setting strategy and budgets under a process called the Quadrennial Defense Review, which was mandated by statute. The Pentagon's new leadership was assessing which weapons systems it ought to buy, how much money ought to be requested, and whether the number of soldiers, sailors, airmen, and marines should be changed.

But in the midafternoon, one of Rumsfeld's top aides frantically called Vickers, telling him that the secretary urgently needed him for a different assignment, one that drew on his storied terror-fighting career from his Cold War days. Soft-spoken and wearing thick glasses, Vickers was the Pentagon's own version of Clark Kent, an unassuming figure whose spare but unusually impressive official Pentagon biography only hinted at the extraordinary life he had lived in the 1970s and 1980s: "His operational experience spans covert action and espionage, unconventional warfare, counterterrorism (including hostage rescue operations), counterinsurgency, and foreign internal defense." Mild manner notwithstanding, Vickers was one of the nation's most experienced counterterrorism operatives and planners.

In 1973, when he was twenty years old, Vickers had enlisted directly into the Green Berets, taking advantage of a rarely offered program that admitted qualified civilians straight out of college or private life into the Special Forces. In Germany, with the 10th Special Forces Group, he learned how to operate behind Soviet lines to link up with partisan forces. The Soviet Union and its Warsaw Pact allies had positioned a vastly greater number of tanks and armored troop carriers along the Fulda Gap in central Germany, across from American and NATO forces. If it came to war, one of his unit's most sensitive missions would be to infiltrate behind Soviet lines, each four-man team armed with a backpack-size nuclear bomb. Vickers and his comrades were to plant these miniature nuclear warheads near massed Warsaw Pact forces and along their lines of attack to blunt their overmatched numbers. But, given the sensitivity of the nuclear technology, the orders were not to drop and run but to maintain "positive control" over the nukes until the detonate directives were broadcast via coded message. Vickers and his men had spoken with the weapons designers and knew the detonation sequence. There was much gallows humor about whether they would have time to get away.

Fortunately, Vickers never had to carry out these orders. Instead, he took advance training and became a Special Forces officer and shifted to Central America, where he combated Salvadoran rebels and helped resolve an airline hijacking and another hostage situation involving Honduran government ministers. Vickers loved the dangerous, fast-paced missions, and when advancement in the Army hierarchy threatened to limit his opportunities to conduct field operations, he packed his rucksack and transferred to the CIA in 1983. By now Vickers spoke Spanish, Czech, and some Russian and was qualified to plan and lead the most sensitive covert operations. In his first year at the agency he was quickly dispatched to the Caribbean island of Grenada to fight alongside Army airborne forces sent to help restore a pro-Western government that had been overthrown by Cuban-backed insurgents.

No sooner had Vickers finished in Grenada when the agency sent him to Beirut in the aftermath of the suicide truck bombings there in October 1983 that killed 241 American service members and 58 French paratroopers. It was Vickers's first brush with Hezbollah, the Iranian-backed, anti-American terrorist organization. But his most heralded mission was yet to come. In late 1984, he was tapped to be the principal strategist for the largest covert action program in the CIA's history: the paramilitary operation to funnel guns, antiaircraft missiles, and money to the Afghan mujahideen that in time would drive the Soviet Army out of Afghanistan. Vickers was featured in the book Charlie Wilson's War and was introduced to film audiences in the Hollywood version as the whiz kid playing chess against three opponents at once in a park across from the White House. But that was artistic license: Vickers does not play chess, at least not the kind on a board with sixty-four black and white squares. From the late summer of 1984 to the spring of 1986, Vickers worked with the Afghan resistance and came to know dozens of Afghan commanders, many of whom on 9/11 were allied with the Taliban or fighting against it.

Few if any American officials understood Afghanistan's history, rugged terrain, and complicated set of warring personalities on 9/11 better than Michael Vickers. And, now more than a decade after his greatest professional triumph, Vickers was being summoned back to help combat a threat in Afghanistan, this time as a civilian adviser to the secretary of defense—a role that would open a second major chapter in his counterterrorism career. But he was still a little out of date in his knowledge, having left the CIA in the spring of 1986 to attend Wharton Business School and having spent the 1990s in academia, the private sector, and the think-tank community. "My view of terrorism was shaped by my experiences in the '80s, which were hijackings, largely Palestinian terrorism," Vickers said. "On 9/12, I had a lot of catching up to do in a hurry."

* * *

The day began at 3:30 a.m. for the thirty-year-old Defense Intelligence Agency (DIA) analyst who, just a few years out of a prestigious midwestern graduate school, had already earned a spot within a tiny, elite cadre of Al Qaeda specialists in the U.S. government. September 11 had started auspiciously for the analyst, who will be identified in this book as John Tyson because of the highly sensitive nature of his intelligence work. He was in early that day to brief his boss, Rear Admiral Lowell E. Jacoby, the Joint Staff's top uniformed intelligence officer, on a complicated stream of information about a terrorist threat that Tyson and some other analysts were tracking. The Joint Staff is made up of 1,300 uniformed officers, enlisted troops, and civilians who work grueling hours in the Pentagon to support the chairman of the Joint Chiefs of Staff, the military's top officer and senior military adviser to the president and secretary of defense.

Shortly after 5:30 a.m., as the briefing wrapped up, the admiral summoned him for a private word. The National Security Council's top counterterrorism official, Richard A. Clarke, had asked for Tyson to join his staff at the White House. Tyson was pleased. During graduate school, he had studied briefly in Egypt and had researched terrorism under the tutelage of a retired police detective who had migrated into academia and specialized in international criminal justice. Tyson joined the DIA in 1997 as the agency's first analyst dedicated solely to assessing the threat posed by a little-known Saudi radical "with a lot of money and a big mouth"—a man named Osama bin Laden. He became a member of a small, eclectic group of bin Laden experts whose ranks included a gruff National Security Agency code breaker; a churchgoing, cat-loving CIA terrorism specialist; and a mother of six who in her day job at the State Department drew on lessons from child rearing to help master the understanding of an emerging terrorist organization called Al Qaeda. Tyson, with his earnest enthusiasm, close-cropped military haircut, and athletic build, was the rookie of the group. Now, he would be working at the White House, the pinnacle of decision making in the government. But the events of that morning would cancel those plans; Tyson was too valuable for the DIA to spare.

At 8:46 a.m., American Airlines Flight 11 plowed into the North Tower of the World Trade Center, and Tyson's world turned upside down. He and other American intelligence analysts had worked through Al Qaeda's attacks on the U.S. embassies in Kenya and Tanzania in 1998. They had worked through the bombing of the USS Cole in 2000. "The Cole attack, where they tried to kill our guys—you take that pretty personal, because we are the Department of Defense," Tyson said. Now 9/11. "They tried to kill me here in this building—you take that personal a little bit, too," he added. "There's something in the pit of your stomach because we'd been waiting for something like this."

Trained for this kind of emergency, one group of DIA analysts immediately began assessing what had happened; another group started going back through classified intelligence reports searching for previously undetected clues about how the attack was planned and conducted; and yet another group reached out to colleagues at the CIA and other intelligence agencies to swap information. That's what Tyson was doing when the Pentagon was hit at 9:37 a.m. "Biggest office building in the world. It is all made of concrete. And to feel it shift, almost like it went up and then back down again, was pretty jolting," Tyson said. After the attack, Tyson drove across the Potomac to the DIA's main headquarters at Bolling Air Force Base in Washington. A few hours later, he was summoned back to the Pentagon. Armed military personnel had to come from a Pentagon command center to vouch for him at the heavily guarded entrance and to escort him back into the building, where he worked and slept that night. "The next year was basically a blur," he recalls.

* * *

These four individuals—Schloesser, Zarate, Vickers, and Tyson—are largely unknown to the general public, toiling one or more levels below the most senior officials in the Bush and Obama administrations. But they represent a cadre of counterterrorism specialists from a variety of backgrounds in the military, law enforcement, intelligence services, and other government agencies who found themselves playing key roles after the 9/11 attacks. Over the past decade, they and others like them have struggled to devise—and sometimes improvise—policies and strategies to fight a persistent and ever-changing, but not always very effective, terrorist foe. Often these were the people who had a first glimmer of a more expansive approach to combating the terrorists and their guiding ideology but were frustrated until some piece of insight broke through and took hold. Their personal experiences over the past ten years offer a glimpse into the evolution of America's fight against Al Qaeda and affiliated terrorist groups.

With skill and luck, the United States was able to avert another large-scale, high-casualty attack in the first years after 9/11. Yet the fact remains that even with improved defenses and increasingly effective tactical success, in the faraway safe havens of Pakistan and Yemen a determined and creative terrorist plot is certain to succeed sooner or later. America cannot be good enough and lucky forever. Had a young Nigerian man been more adept in detonating an explosive sewn into his underwear on Christmas Day 2009, an American commercial jetliner would likely have crashed in Detroit, killing hundreds of people. Had a Pakistani American honed his bomb-making skills just a bit better, his SUV packed with explosives would have detonated in Times Square in May 2010. Had that plot, hatched in Pakistan's tribal areas, succeeded, it likely would have forced the Obama administration to attack targets in Pakistan in ways that would have had exceedingly negative and enduring ripple effects on American policy in the Muslim world.

In many ways, the best the United States can now do is to push that day of reckoning farther down the road, reduce the possible damage inflicted by a strike, and build a national resilience akin to what the British and the Israelis have developed over time and through grim experience: to recover quickly and confidently from the terrorist attack that is sure to come. But to make this happen, the American public needs to know more about what those in our counterterrorism structure know—and what they fear.

* * *

The memory remains strong throughout the U.S. government of how ill-prepared it was on 9/11 to cope with the threats of modern terrorism. The commander in chief, President George W. Bush, was aboard his vaunted flying command post, Air Force One, for most of the day, but its Cold War command-and-control capability made it virtually useless for the requirements of this twenty-first-century threat.

Air Force One was built to protect the president and broadcast launch codes in the event of a nuclear war, not to operate as an airborne information hub and media center. Getting live television and Internet aboard the aircraft had never been a priority and was not possible on September 11. Bush, who had begun the day in Florida and was fuming that he could not return immediately to Washington, was infuriated that he could not receive a live feed from Fox News, CNN, or any other cable television network. The president, his aides, and reporters on board were left squinting at soundless, fuzzy images skimmed from weak ground signals of local television channels below as the presidential plane passed overhead. Despite the investment of hundreds of billions of dollars in the country's military arsenal and spy networks, Bush was largely blind to the vivid images of destruction and disarray that were seen by millions of Americans live on television.

To protect the president after the attacks in New York and Washington, Air Force One zigzagged west on a secret route from Florida to Barksdale Air Force Base in Louisiana to refuel. On the tarmac, Bush was unnerved by what he saw outside his window: rows of B-52 nuclear bombers were on the runway in scramble mode, and air crews were running around in battle-dress uniforms. The airmen were not gearing up in response to the terrorist attacks, it turned out, but were part of a previously scheduled annual drill by the U.S. Strategic Command, simulating a nuclear attack against the homeland. Barksdale did not possess the technology to connect the president by secure videoconference with his top advisers in Washington, so Air Force One was quickly airborne again, this time bound for Offutt Air Force Base outside of Omaha, Nebraska, the headquarters of the Strategic Command, or "Stratcom." Deliberately located in the middle of the country during the Cold War—at that time out of reach of Soviet long-range missiles and bombers—Stratcom and its subterranean war room were built to transmit a president's orders to launch a nuclear strike.

Stratcom had been engaged for more than a week in a high-level exercise called Global Guardian, which posited that a rogue nation called Slumonia would attack the United States with nuclear weapons. The State Department insists that countries cast as adversaries in war games not be identified, but Slumonia was a small nuclear power in northeast Asia—obviously, North Korea. With the cancellation of constant high alerts at the end of the Cold War, American bomber crews did not have extensive experience in loading nuclear weapons, so this exercise was a way to keep their skills up to date. That is why on the morning of 9/11 air crews were pulling nuclear bombs and missiles out of their heavily guarded storage sites and loading them aboard B-52s and B-2s in Louisiana and Missouri—precisely the scene that startled Bush at Barksdale. The nuclear weapons were real, but their triggers were not armed.

By the time Bush landed at Offutt, Admiral Richard W. Mies, Stratcom's commanding officer, had cancelled the training exercise and ordered the nuclear warheads returned to secure storage bunkers and the bombers dispersed, lest either pose a target of opportunity for an unforeseen follow-on terrorist attack. "We are not under pretend attack," Mies told his assembled staff. "We are really being attacked."

Even as Stratcom was rehearsing for old-school threats, the military's elite counterterrorism force, the Joint Special Operations Command at Fort Bragg, North Carolina, was preparing to conduct an exercise against the growing threat of a nuclear, chemical, or biological terrorist attack against the United States or against American interests. On September 11, about 1,800 Special Operations forces and a handful of other secret government operators were preparing to launch a sixteen-day exercise in six European and Mediterranean countries and on a ship at sea. The goal of the classified drill was to find and thwart terrorists who had captured an unconventional weapon and threatened to use it against the United States. The exercise, overseen by the U.S. European Command and code-named Ellipse Charlie, was called off that day during its final planning stages, and the commandos rushed back to their real-world bases.

The European Command and the Special Operations forces had identified the right kind of threat. Because they were trained in hostage-rescue operations and counterterrorism missions, it also made sense that the Special Operations troops were rehearsing a complicated mock attack from a foe like Al Qaeda. But the American commandos and the rest of the U.S. government were still several steps behind Al Qaeda in piecing together the critical intelligence and threat information that could have helped prevent the attacks. Now the race was on to learn everything possible about Al Qaeda before it could strike the homeland again.

* * *

On Monday, October 15, Jeff Schloesser steered his dark green BMW onto Interstate 95 and started the thirty-minute trip from his home in Springfield, Virginia, to the Pentagon. At 5:30 a.m., the crushing Washington morning commute had not yet turned the eight-lane freeway into a parking lot, and Schloesser made good time on this crisp morning, the first day of his new job and a world away from the Middle East.

In the five weeks since 9/11, Schloesser had returned from his fifteen-month assignment in Kuwait, expecting to go to Washington to punch the next ticket in his climb up the Army's leadership ladder: a stint working European policy issues on the military's Joint Staff. Schloesser had served in Kosovo in the late 1990s, giving him some exposure to the bedeviling intricacies of Balkan politics. But Schloesser's boss, Lieutenant General John Abizaid, had other ideas for him. Abizaid directed political-military affairs for the Joint Staff and was one of the Army's most intelligent officers. A Lebanese American with small-town roots in northern California—and the only Arabic speaker to advance to four-star rank in the Army (he would get his fourth star in 2003)—Abizaid had served in Jordan and had spent a year as a member of a UN observer force in southern Lebanon. In between those assignments, Abizaid had commanded a 120-man Ranger company that parachuted into Grenada as part of the 1983 invasion. At one point in the operation, Abizaid ordered a soldier to hot-wire a bulldozer at the airfield and charge at Cuban troops with blade raised, giving cover to himself and his men (an incident that was immortalized in the 1986 Clint Eastwood film Heartbreak Ridge). Schloesser reported to Abizaid's office early that morning, not knowing exactly what was in store for him. "Forget Europe," Abizaid said. You're going to stand up a brand-new office here, the Strategic Planning Cell for the War on Terror."

In wartime, the responsibility for planning and waging specific campaigns falls to the regional military commander assigned to oversee that slice of the globe. In this case, responsibility for Afghanistan fell to the U.S. Central Command, based in Tampa, Florida, and led by General Tommy R. Franks. The broader strategic military planning that cuts across different regional commands is the domain of the Joint Staff. On September 11, the Joint Staff had no office or staff specifically assigned to thinking about fighting terrorists around the world. Jeff Schloesser and his new team would be filling a crucial void.

At the end of the week, Abizaid convened his crisis-action team and singled out his newest chief terrorist hunter. "Have we killed any Al Qaeda yet?" Abizaid demanded, staring at Schloesser. Schloesser, still trying to find his way around the labyrinthine halls of the Pentagon, wrote that night in one of the small, green notebooks that he kept for every assignment since he was a young captain: "Not sure, too much focus on the Taliban in Afghanistan and not enough on our global fight against Al Qaeda." Schloesser was not alone in grappling with America's newest Public Enemy Number One.

* * *

Within the U.S. government on September 11, 2001, there were peaks and valleys in terms of understanding Al Qaeda, but mostly valleys. The Clinton administration had reacted with increasing alarm after Al Qaeda's attacks in 1998 against the U.S. embassies in Kenya and Tanzania as well as the strike on the Cole two years later. But President Clinton never ordered more than cruise missile strikes against Al Qaeda targets. When George W. Bush took office in January 2001, few of his advisers had any detailed understanding of how Al Qaeda was organized, how it was equipped, and how it could train its operatives to carry out the worst attack on American soil since Pearl Harbor. As one senior White House official who closely monitored terrorist intelligence reports recalled, "There were people up and down the hallways who couldn't spell Al Qaeda. Literally they didn't know a thing. I remember being asked, ‘Is it all one word or two?'"

The new administration's greater national security concerns centered on building antimissile defenses against a rogue state like North Korea or countering the growing military influence of China throughout Asia. After September 11, there was a mad scramble to catch up. Within the inner circles of the Bush administration, officials vented frustration at the lack of clear understanding about the nature of this new enemy. At the same time, intense debates involving senior policy makers and intelligence officials centered on how precisely to define the enemy beyond Al Qaeda. "Pretend it's a box," explained one participating intelligence official, recounting a primer he gave to senior White House aides. "Who is inside the box and who is outside the box with this enemy? Is it Hezbollah? Is it Hamas? There is a lot of debate about how big this box is and what you put in it."

In the months after the 9/11 attacks, government officials arrived at a tentative consensus about transnational threats with global reach. Al Qaeda and its associated groups became the main target. But intelligence officials and policy makers struggled with how to define the nature of the enemy, where it resided, and its nexus to state actors, including Iran, Sudan, and Iraq. It was a question that grew increasingly politically charged beginning in early 2002, as senior Bush administration officials sought to draw links between Al Qaeda and the government of Saddam Hussein in Baghdad.

In the initial weeks after the attack, the more than fifty organizations that make up the U.S. government's intelligence and law enforcement agencies scrambled to try to answer these questions. But often they found they spoke past each other, had different priorities, and played diverging and uncoordinated roles in combating the new threat.

At the National Security Agency, the supersecret eavesdropping agency at Fort Meade, Maryland, a call went out from its director, Lieutenant General Michael V. Hayden of the Air Force, to open the spigots and provide as much information as possible to the FBI, which was responsible for tracking terrorists inside the United States. Little of the NSA's technical wizardry had been aimed at Al Qaeda before 9/11. As FBI agents chased tips culled from telephone, e-mail, and other communications intercepts, many of them complained that the NSA's information was nothing but a series of dry holes that wasted critical manpower and resources. The NSA fired back that the FBI had misused and misunderstood the valuable clues they had been provided. It didn't help that the FBI lagged woefully behind in updating its outmoded computer systems. "We in no way thought we were giving them leads," Hayden said. "We thought we were giving them raw data that they would put into a larger database. It took us a period of time to go, ‘Oh, hell, that's not working. Tighten it up here,' because they just didn't have the ability to absorb what was coming down."

But the nation was on edge, fearing another wave of attacks. In this heightened threat environment, the CIA began dumping its in-box of raw intelligence reports of plots, sightings, and potential attacks on Bush's desk every morning as part of his top-secret Presidential Daily Briefing. The data came in a neatly printed spreadsheet called the Threat Matrix, the top two or three dozen of the most disturbing pieces of intelligence and suspected plots that American and allied spy agencies had dug up in the previous twenty-four hours. "In those early days, believe me, we saw them all—nuclear, biological, chemical [NBC]," said a former senior staff member of the National Security Council. "There were compelling reports of NBC being developed, smuggled in, and planned for use in the U.S. None of them panned out, but it all affected the psyche of policymakers after 9/11."

As the FBI and NSA crossed signals early on, the FBI and the CIA also operated at cross-purposes, sometimes unwittingly. In order to avoid being shunted aside in advising the president on threats to the nation, the FBI soon came up with its own version of a threat matrix for the president. At one point in early 2002, both agencies were tracking what American analysts said were growing preparations for a major "wedding" somewhere in the Midwest. In terrorist parlance, the word wedding is often code for a major attack. Dribs and drabs on this "wedding" planning made their way to the president from both agencies, independent of each other, of course. Finally, over the Easter holiday, during a video-teleconference with top aides in Washington from his ranch in Crawford, Texas, Bush halted the briefing, exasperated by the discrepancies in the rival agencies' reporting about the suspected threat. "George, Bob, get together and sort this out," he told his CIA director, George J. Tenet, and FBI director, Robert S. Mueller III.

Bush's instincts were right. When the analysts finally untangled their clues, it turned out that the ominous "wedding" really was just that: the matrimony of a young man and a young woman from two prominent Pakistani American families. There was no threat. There was no plot. Until the president personally intervened, however, the FBI and CIA had jealously guarded their sources and assessments without collaborating to resolve what turned out to be a time-consuming dead end.

* * *

Within three months of the 9/11 attacks, the Taliban had been routed and had fled Afghanistan. Osama bin Laden had escaped the bombing of Tora Bora and slipped across the border into Pakistan. Mindful of the lessons of the Soviet occupation in Afghanistan, the Americans maintained a light footprint there: small groups of CIA paramilitary officers supported by Special Operations forces that worked closely with the indigenous Northern Alliance troops. At the Pentagon and at the CIA, analysts and operatives watched as militants spilled out of Afghanistan and scurried for refuge elsewhere, plotting to fight another day. Yet the outlines of what constituted Al Qaeda and its affiliates were still vague. A fear of when and where the next attack might take place continued to grip official Washington. With little information or understanding of how extremist networks like Al Qaeda work, some proposed responses by various agencies were driven by overreaction or worse.

Some planners proposed that if Al Qaeda appeared ready to attack America again, the United States should publicly threaten to bomb the city of Mecca in Saudi Arabia, the holiest site in all of Islam, in retaliation. "Just nuts!" one sensible Pentagon aide wrote to himself when he heard the proposal. This plan, while far-fetched, copied traditional Cold War deterrence in laying out punishment in advance to deter an attack. While this proposal was quickly rejected, more refined and realistic versions would come along in its place.

Also in the Pentagon, Jeff Schloesser and other planners used the visceral image of cutting off the head of the snake to describe their goal. Kill or capture the leaders of Al Qaeda, the strategy dictated, and the organization would wither and die or at least be seriously disrupted and less able to launch major attacks against the homeland. In those early days after 9/11, the government struggled to coordinate the disparate counterterrorism efforts, from CIA clandestine missions to NSA electronic eavesdropping. The Pentagon, with its vast budgets and ability to marshal manpower around the globe, sought a leading role. By early December 2001, the Pentagon's top policy official, Undersecretary of Defense Douglas J. Feith, had directed Schloesser and his team to prepare a highly classified plan, called Next Steps. The briefing, culled from the recommendations of combatant commanders around the world, outlined a series of secret military operations against Al Qaeda and its affiliates in more than a dozen countries, including Yemen, Somalia, and Sudan.

Feith, a Georgetown University–trained lawyer and self-acclaimed big thinker, was drilling down into the nitty-gritty details of military and intelligence operations against Al Qaeda cells worldwide. Schloesser and other military planners on the Joint Staff were early and ardent advocates for a longer-term strategic plan for the military to combat terrorism, a project normally expected to flow from the Pentagon's top civilian policy maker. But in this case the call for strategy flowed in the opposite direction. Feith supported the idea, but feeling pressure from Rumsfeld, he was focused on the immediate threat and specific missions to counter it.

"When we would go up and do an early conceptual brief on what we thought the national military strategic plan would be, Feith would say okay, that's fine, but let's talk about what we're going to do next month," Schloesser recalled. "What are we going to do in Indonesia? What are we going to do in Mali? What are we going to do in the tri-border area of South America? He was very tactically oriented."

The Next Steps planning quickly took shape. In Somalia and Yemen, countries with weak or virtually no effective central governments capable of identifying and attacking Al Qaeda cells, plans were set in motion to deny safe havens to Al Qaeda and other terrorists. Teams of Special Operations forces and CIA paramilitary officers would target militants with nighttime raids throughout the world. In the Mediterranean, Navy warships would step up patrols to disrupt terrorists' logistics and snatch militants at sea.

In the Philippines, a new program was envisioned to help train and equip the Philippine military and security force to combat the Abu Sayyaf group, an Islamic militant group linked to Al Qaeda in the southern part of a country made up of over seven thousand islands. In Bosnia and Kosovo, commanders proposed combining an ongoing mission to hunt war criminals from the Balkan wars with a new plan to track Islamic extremists.

Deputy Secretary of Defense Paul D. Wolfowitz sounded a warning note to nations that might be harboring or otherwise helping terrorists, echoing the "with us or against us" theme that President Bush had articulated in the days after 9/11. At the same time, a handful of influential commanders and analysts began expressing concerns that this strategy would not be enough to slay the terrorist organization and keep its ideology and appeal from spreading. Top commanders like John Abizaid acknowledged that these first series of steps after 9/11 to isolate terrorists in a handful of kill zones in other countries were unrealistic, because of a lack of precise intelligence, a lack of trained forces on the ground, and little understanding of how emerging terrorist cells operated. "We thought we could take our counterterrorist forces, move them decisively to the right place and kill the right people at the right time," Abizaid explained. "We started to understand very quickly that the intelligence wasn't good enough to allow us to have a campaign like that. So people are looking for a method to be able to engage, disrupt, defeat terrorist actions."

"Our ideas about this enemy were very rudimentary at the time," said Abizaid. "It wasn't because the professionals that were working on them were bad guys or they were incompetent. It had nothing to do with that. There were very, very few people in the government that were dedicated to the problem, and all of a sudden the shift in our focus showed there were huge intelligence gaps."

One example illustrates both the bold thinking and wildly unrealistic aims of the military's initial approach. The plan called for hunting eight to ten senior Al Qaeda leaders and operatives, including at least one of Osama bin Laden's sons, who had sought refuge in Chalus, an Iranian resort town on the Caspian Sea. In the chaotic days leading up to the fall of Kabul, Afghanistan, in November 2001, Osama bin Laden and Al Qaeda's top leadership made a pivotal decision about its future. Al Qaeda's leadership had been divided into management and consultative councils, or shuras, both of which reported to bin Laden. The management arm, the most important element in the terrorist group's continued operations, which included bin Laden and his top deputy, Ayman al-Zawahri, would flee east into Pakistan's rugged tribal areas and teeming cities.

The consultative arm, which included the son, Saad bin Laden, would go west, to northern Iran, where American troops could not pursue them and the Iranians would likely not detain them. The younger bin Laden was a member of Al Qaeda and had been part of a small group of Al Qaeda operatives who fled from Afghanistan and would later become involved in managing the terrorist organization from Iran. But the Shiite clerics running the country placed the Al Qaeda operatives and their family members under virtual house arrest, and they became a shield against possible future attack from the Sunni-based terrorist organization.

At the Joint Special Operations Command (JSOC) at Fort Bragg, military planners drew up schemes for Navy SEALs to sneak ashore under the cloak of darkness using state-of-the-art mini-submarines called submersibles. Once they landed, the SEALs would slip past Iranian guards to snatch the Al Qaeda leaders. Another option called for Special Operations helicopters to spirit American commandos into the town and whisk them out again with their quarry. The American commandos went as far as conducting two or three rehearsals of a clandestine kill-or-capture mission into Chalus at an undisclosed location along the Gulf Coast of the United States in early 2002. They conducted small-boat insertion exercises involving about thirty Special Operations personnel, mostly SEALs, and eventually concluded the mission was feasible if they were provided with more detailed intelligence on the location of the Al Qaeda members and the security around them.

The logistics of the mission were daunting. Chalus sits at the edge of the Elburz coastal mountain range about seventy miles north of Tehran, and the failed rescue of the American hostages in Iran in April 1980 loomed large in commanders' memories. Eventually, General Richard B. Myers, the chairman of the Joint Chiefs of Staff, rejected the missions as too risky and too politically volatile. In the end, even the JSOC commanders seemed relieved they would not be tasked with such a long-shot operation.

* * *

By March 2002, as the fight in Afghanistan wound down and policy makers in Washington secretly began shifting their attention to Iraq, General Myers was worried that the country was losing sight of the larger global threat posed by Al Qaeda, an enemy that intelligence analysts concluded had the patience, will, and resolve to outlast its Western adversaries. Myers was also deeply frustrated that the early fight against Al Qaeda had been dominated by the military. Myers, a fighter pilot in Vietnam and a student of history, knew that military power alone could not defeat a committed terrorist organization. "You learn very quickly that most insurgencies are not brought to heel through military power alone," Myers said. "It is using political and diplomatic power and economic power. In my view, they have to be applied simultaneously."

But in National Security Council meetings, it was easier to talk about deploying another brigade of the 82nd Airborne Division or a squadron of fighter-bombers than mapping out a coherent political and economic recovery plan for a destitute country like Afghanistan. "It is made harder yet, because other departments and agencies are not as well resourced," Myers said. "And maybe their heart is not in it. Maybe they do not feel the same sense of urgency as the military does because we are dying and we have injured. That was the frustration. It led to the thought that we do not really have a strategy. We do not have an overarching strategy." Myers and his allies in the Pentagon set about exploring a new strategy that built off Next Steps but also called for more involvement by other parts of the government.

In early March 2002, Myers convened a Saturday meeting of his top staff directors. He looked around the table at some of the military's best and brightest officers. "Who in this room thinks we have a strategy to defeat Al Qaeda?" he asked. Not a hand went up. Myers assigned his team to come up with a plan by the following Saturday. When the group reassembled a week later, the officers recommended, as a first step, an all-of-government effort to eliminate Al Qaeda's top leaders and planners, specifically Osama bin Laden and Ayman al-Zawahri as well as seven leading planners and operational commanders. The plan was dubbed Two + Seven and was drafted by John Tyson and his fellow DIA analysts before going to Schloesser, General Myers, and, ultimately, all the way to President Bush's desk. (The original plan was actually called Two + Nine, but two of the Al Qaeda leaders were killed before Tyson could brief senior officials on the new concept.) "Two + Seven was pretty crude," Myers acknowledged later. "It was trying to bring a strategy to what we were doing."

Myers consulted closely with CIA director George Tenet on the list and on how to carry out the goal of crippling or seriously disrupting Al Qaeda's planning and operations. Both sides brought strengths and abilities to the plan. The CIA had skilled linguists, experienced case officers with networks of informants on the ground, and finely honed analytical skills. The military had firepower, unparalleled reconnaissance and surveillance abilities from satellites to spy planes, and seasoned teams of Special Operations forces. The Treasury Department, armed with Juan Zarate's financial sleuths expert at tracking terrorists' financing, weighed in with critical information that helped diagram the web of connections between terrorists and their suppliers, recruiters, and financiers.

Tyson and the other DIA analysts warned their bosses against getting overly enamored of the new plan to wipe out Al Qaeda's leadership. Al Qaeda, they pointed out, had already proved surprisingly adept at replacing its fallen leaders. "If you get these guys simultaneously or in quick order, you're going to have a major impact on the organization," Tyson said. "If you don't, it is going to have an effect, but it will be considerably less."

Senior Pentagon officials brushed the warnings aside. Over the next weeks, Two + Seven became Two + Seven + Thirty, adding another ring of lethal Al Qaeda planners and subcommanders around the world. Each time informants provided enough solid or "actionable" intelligence to target one of the militants on the list, executive orders were drafted and signed by Rumsfeld, sometimes going all the way to the White House for Bush's approval. The president kept an updated copy of the list in his desk and crossed out each name and photograph after a militant was killed or captured. But this case-by-case approach took time, often time the covert forces didn't have before an Al Qaeda commander might slip away. Under Myers's direction, Jeff Schloesser and his Pentagon team looked for ways to speed up the process. They began shepherding through the senior levels of the military, CIA, and National Security Council a list of more than a dozen countries where high-level militants were believed to be operating as well as the preapproved decisions and legal authorities to kill those militants. These authorities were translated into a color-coded matrix that made it clear the military had approval in advance from the president and secretary of defense to attack fleeting targets in countries like Afghanistan. Where more covert means were required, as in Pakistan, the CIA would take the lead. In some countries, such as Iran, there were no preapproved targets. "In the end, it was asking for pre-approval rather than having to go back to the president at three o'clock in the morning," Schloesser said.

Much of the early effort called for mounting continuous counterterrorism operations on both sides of the border with Pakistan. Handfuls of American military intelligence and communications specialists joined Pakistani forces searching for fugitive fighters in the mountainous tribal border areas traditionally outside the control of the government in Islamabad. In addition, small numbers of Special Operations commandos conducted cross-border reconnaissance missions into Pakistan, ready to strike at Al Qaeda fighters. The Pakistani and American forces were treading gingerly, however, since they were operating for the first time in the Pakistani tribal zones and sought to avoid provoking resistance from Pashtun tribesmen who shared ethnic ties with Taliban fighters.

In Pakistani cities, FBI agents helped the local police and provided information—in rare instances even personnel—to break up what senior American intelligence and law enforcement officials regarded at the time as a depleted but still dangerous network. The traditionally independent American military and law enforcement organizations were now working more closely together than they ever had prior to 9/11, sharing information and expertise as Al Qaeda tried to reconstitute itself in Pakistan. The presence of Al Qaeda in the cities was confirmed by intercepts of cell phone, Internet, and e-mail traffic. The commitment of American troops was relatively light, with no more than two dozen Special Operations forces working in the tribal areas at any given time. The operations, including day-and-night raids and methodical sweeps, were carried out by rapidly moving, highly trained allied soldiers with intensive intelligence-gathering elements to kill or capture specific militants.

The strategy of targeting Al Qaeda's senior leaders paid early dividends. In March 2002, the key Al Qaeda planner, Abu Zubaydah, was one of the first terrorists captured by Pakistani authorities and turned over to the CIA for interrogation. In September, Pakistani police raided an apartment in Karachi and captured Ramzi bin al-Shibh, a senior Al Qaeda member, in a gun battle. On November 4, a Hellfire missile fired from a CIA Predator drone in the Yemeni desert killed Qaed Senyan al-Harthi, also known as Abu Ali, one of the planners of the Cole bombing two years earlier. The Yemen strike was the first time an armed Predator drone had been used to attack suspected terrorists outside of Afghanistan. It also signaled a more aggressive phase in the campaign against terrorism, with the United States relying less on the cooperation of other nations to arrest and detain suspected terrorists when they were discovered overseas. But the most important Al Qaeda leader on the Two + Seven list to be seized was Khalid Shaikh Mohammed, generally recognized as the third-ranking official in Al Qaeda and one of the principal planners of the East Africa embassy attacks, the Cole bombing, and 9/11 itself. Pakistani forces seized him during a raid on a house in Rawalpindi on March 1, 2003.

As time went on, the seven terrorists initially linked with bin Laden and al-Zawahri on the Two + Seven chart were killed or captured, and new names turned up on President Bush's scorecard. The initial strategy was chipping away at the enemy's leadership, but an approach broader than kill-or-capture was clearly needed.

Another problem remained unresolved: Who would lead that effort? The president, of course, was ultimately in charge of what he called the "war on terror." But day-to-day, who would take the lead and have the responsibility and authority? "Who was in charge of the war on terror from 9/11 to now?" Myers would later reflect. "I'd say there was probably nobody in charge." The military was still locked in a kill-or-capture mentality, but elsewhere in the government new thinking on combating terrorists was emerging.

* * *

In the months after 9/11, the FBI was undergoing a seismic shift in combating terrorism at home and abroad. From the days of J. Edgar Hoover's G-men, FBI agents had risen through the ranks by arresting bank robbers, kidnappers, and white-collar criminals. But the bureau was transforming fitfully after the 9/11 attacks and now ranked fighting terrorism as its number-one priority. It doubled the number of agents assigned to counterterrorism duties to roughly five thousand and created new squads across the country that focused more on deterring and disrupting terrorism than on solving crimes.

The FBI was no stranger to domestic terrorism. The bombing of the Alfred P. Murrah Federal Building in Oklahoma City on April 19, 1995, by Timothy McVeigh killed 168 people. And the first World Trade Center bombing on February 26, 1993, by Ramzi Yousef, the nephew of Khalid Shaikh Mohammed, killed six people and injured more than a thousand others. But counterterrorism remained a highly specialized backwater at the bureau. On September 11, fewer than one hundred agents had the know-how, field experience, and background running national programs to coordinate a multidistrict, multiagency, international operation like the investigation after 9/11.

A major lesson from the first World Trade Center bombing was to keep the terrorists off balance and disrupt their plots before they could carry out the next big one. In the initial weeks and months after 9/11, with government experts concerned about a second wave of terrorist strikes, there was a full-court press to anticipate and interdict any follow-up attacks.

As top FBI counterterrorism officials saw it, if they did not detect a plot unfolding and identify the potential plotters, they needed "to shake the trees hard and make sure that anybody that looks like or smells like or breathes like a terrorist is not given the opportunity to execute on an operation that we don't see." That strategy came at a cost. By 2003, some counterterrorism experts within the FBI began challenging whether disruption alone was the best strategy to combat terrorists. "What we began to realize pretty rapidly was that there was a lot at stake when you disrupt somebody and you really don't have a clear picture of what their involvement is or what the network is," said Arthur M. Cummings II, a top FBI counterterrorism official.

Cummings, a stocky former Navy SEAL, worried that while arresting a suspected or known terrorist would remove that particular threat, it might also leave authorities blind to a larger terrorist network and its ongoing operations. "When we have somebody who is a terrorist come to American borders, the question always should be asked: Are we losing more than we're gaining in this disruption strategy?" he said. "Do we have a view into the genuine nature of the enemy and what they plan to do and what their network is and what facilitation capacities they have within the United States? Does that exist? Do we have that knowledge?"

In 1995, when American and Pakistani authorities arrested Ramzi Yousef in Islamabad, the federal agents who brought him back to the United States for trial questioned him for six hours on the flight. Most of the questions focused on Yousef's culpability and building a body of evidence that would hold up in court. "He was proud of what he did, he gave us a ton of evidence, all of which was Mirandized and all of which we could use in court," Cummings said. "What we didn't understand about Ramzi Yousef was that basically he could have told us what the future of Al Qaeda was going to be, what the leadership of Al Qaeda was going to be, what their aims were, where their aims were going to focus, what was the future of this organization." Before 9/11, the FBI focused on the individual and building a case against him. "If you take that paradigm and you completely turn it around, and you take a saw and buzz around his head and peer in, that is your new objective," Cummings said. "I don't care about the man. Ramzi Yousef is of no interest to me except that he is a means to my understanding of the broader network."

By late 2002 and 2003, FBI counterterrorism officials were pressing state, local, and federal law enforcement authorities to answer a series of questions before making any arrests. For Cummings and a growing cadre of counterterrorism specialists in the bureau, teasing out the contours of a potential terrorist network became more important than making an immediate arrest. "Do you know everything there is to know about this individual and his network and his area of influence? And if you don't, and if he is not an imminent threat, why are you taking him off the street and why are you effectively going blind?" Cummings said. "And that blindness is going to hurt us in the long run."

With some resistance from old-guard agents, the new paradigm began to take hold and have a pivotal impact on the daily morning intelligence briefings convened by FBI director Mueller and on special briefings with Attorney General John Ashcroft. Cummings and other champions of the strategy called it risk management. Once the FBI, through electronic surveillance, informants, or information from foreign partners, realized that a known or suspected terrorist was operating in the United States, the question became: How long do you track him in order to identify his contacts and map his "pattern of life," all the while risking that the suspect might slip his surveillance, before arresting him and possibly closing whatever window authorities had into an emerging plot? "Before, it would be that our focus was only on developing evidence, facts that were admissible in a courtroom," Mueller said. "Yes, you have to identify those that may end up in a courtroom but beyond that you have to paint a full picture of what is going on."

Local authorities were also engaged in taking steps to interdict terrorist attacks. New York City beefed up its intelligence and counterterrorism capability after 9/11. In March 2003 the New York Police Department (NYPD) dealt with a plot to severely damage the Brooklyn Bridge involving Iyman Faris, a thirty-four-year-old naturalized American citizen from Kashmir living in Columbus, Ohio. Faris had been under federal surveillance, and when the police were informed of the potential threat, they increased marine and land security coverage around the bridge. Faris concluded that the plot was unlikely to succeed—apparently because of increased security—and aborted it. He was arrested shortly after that. "We made a very visible presence there, and that may have contributed to it," said Paul J. Browne, the chief spokesman for the NYPD. "Deterrence is part and parcel of our entire effort."

In New York City today, as many as one hundred police officers in squad cars from every precinct converge twice daily at randomly selected times and selected sites, like Times Square or the financial district, to rehearse their response to a terrorist attack. Police officials say the operations are a crucial tactic to keep extremists guessing as to when and where a large police presence may materialize at any hour. Borrowing a page from the playbook of authorities in London, the police in New York are working on a plan to track every vehicle that enters Manhattan to intensify the city's vigilance against a potential terror attack. Data on each vehicle—its time-stamped image, license plate imprint, and information on whether it is releasing radio waves or even radiation—would be sent to a command center in Lower Manhattan, where it would be indexed and stored for at least a month as part of a broad security plan that emphasizes protecting the city's financial district.

Federal agencies were also realigning their focus on counterterrorism, expanding beyond the military's kill-capture focus to hone new measures to deter terrorist activity. At the Treasury Department, Juan Zarate was piecing together the remaining law enforcement components after the Secret Service and the Customs Service were incorporated into the new Department of Homeland Security in 2002. Zarate laid out an ambitious plan to make Treasury a pivotal player in the government's post-9/11 counterterrorism arena, leading the global effort to track down Saddam Hussein's assets; working with important Middle East allies such as Saudi Arabia, Pakistan, and the United Arab Emirates to crack down on terrorists' use of financial networks in those countries; and with David Aufhauser, Treasury's general counsel, creating the Office of Terrorism and Financial Intelligence in 2004, with the first intelligence shop inside any finance ministry in the world.

* * *

By the middle of 2002, the focus of political leaders in Washington and military commanders in the field was shifting dramatically toward Iraq. Scarce military resources like reconnaissance and surveillance planes, Predator drones, and Special Operations forces were being readied for the invasion to come.

For many policy makers, including Vice President Dick Cheney and Deputy Secretary of Defense Wolfowitz, the various threats often had tantalizing though vague connections to Iraq, a threat they saw as larger than the one posed by Al Qaeda. By late November, Jeff Schloesser had been assigned to write a classified internal assessment, entitled "Leveraging Iraq," that sought to forecast how toppling Saddam Hussein's government would influence the behavior of state sponsors of terrorism, notably Iran, Syria, Libya, and Sudan. When Schloesser questioned the timing of a potential military campaign against Iraq, Myers snapped at him, "Get with the team."

Schloesser's frustration, however, was understandable. The Two + Seven chart that Bush kept in his desk kept acquiring new names and mug shots in addition to those of the maddeningly elusive top two leaders. There seemed to be an endless supply of replacements to plot new attacks. Schloesser's concern was prescient. Seven months later, on May 16, 2003, a series of suicide bombings ripped through Casablanca, Morocco, killing forty-four people. On March 11, 2004, bombs exploded on four trains at three stations in Madrid, killing 192 people and wounding about 1,800.

Efforts to rouse a "whole-of-government" approach were gaining little traction, despite the growing evidence that the administration needed to devise a more creative strategy to enlist popular support in places like Iraq, Afghanistan, and the broader Middle East to dry up the seemingly endless stream of young recruits and money flowing to the terrorist networks. While the president spoke of "a nation at war," it was really a military at war, along with its partners in the intelligence community. Efforts to combat Al Qaeda's ideology and narrative that the West was at war with Islam—the so-called war of ideas—got short shrift in the meetings of Bush's top national security aides.

After a White House meeting on December 13, 2002, Myers returned to the Pentagon in a foul mood. Bush had made it clear to him and to his other top national security officials that the way to victory was killing and capturing the enemy. "He doesn't have much patience for the battle of ideas," Myers told his aides after the meeting. Bush's edict to his top military and civilian advisers came just a week after Donald Rumsfeld had written a memo to the president, warning him that the United States was losing the pivotal ideological war of ideas against Al Qaeda. It would be several more years before Bush changed his thinking, losing critical time and focus on what ultimately became one of the U.S. government's main efforts to combat terrorists.

By the summer of 2003, just a few short months after the giddy early days of battlefield success in Iraq and Bush's declaration of "Mission Accomplished," any aura of victory was beginning to fade as a shadowy insurgency in Iraq stepped up its attacks on American forces. At first, Rumsfeld denied that the American forces were facing any kind of guerrilla force in Iraq. But on July 16, John Abizaid, now a four-star general who had just taken over the Central Command from Tommy Franks, acknowledged for the first time that American troops were, indeed, in a "classical guerrilla-type" war against the remnants of former Iraqi president Saddam Hussein's Baath Party. These fighters had organized cells at a regional level and demonstrated the ability to attack American personnel with homemade bombs and tactical maneuvers. Abizaid warned that the Baathist attacks were growing in organization and sophistication, and he also cited a resurgence of Ansar al-Islam, a fundamentalist group the State Department said was tied to Al Qaeda, and the appearance of both Al Qaeda and Al Qaeda look-alike fighters on the battlefield.

The Bush administration's justification for the war in Iraq at first hinged on fears that Saddam Hussein was developing and stockpiling weapons of mass destruction, possibly to share with terrorists. When no such weapons were found, the administration's rationale for toppling the Iraqi government shifted toward bringing democracy to the Middle East. But now, foreign fighters were being drawn to Iraq to fight the Americans. Iraq may not have been the central front in the war on terror immediately after 9/11, but it was now. Two months later, Abizaid briefed senior administration officials, allies, and lawmakers on what he called the Long War, which extended far beyond Iraq. "Despite remarkable victories, the fight against terrorism is far from over," Abizaid told the Senate Armed Services Committee on September 25. "The enemy's ideological base, financial networks and information networks remain strong. Indeed, the demographic and economic conditions that breed terrorists may be worsening and those conditions are heightening the ideological fervor associated with radical Islamic extremism." Abizaid told the lawmakers that the Pentagon recognized that the spreading war was not against Islam. "It is not a war against religion," he said. "It is a war against irreligious murderers."

The gloomy message was sinking in. On October 16, 2003, Rumsfeld sent a two-page memo to Wolfowitz, Feith, Myers, and General Peter Pace, the vice chairman of the Joint Chiefs. "Are we capturing, killing or deterring and dissuading more terrorists every day than the madrassas and the radical clerics are recruiting, training and deploying against them?" Rumsfeld asked in the note. "Does the U.S. need to fashion a broad, integrated plan to stop the next generation of terrorists? The U.S. is putting relatively little effort into a long-range plan, but we are putting a great deal of effort into trying to stop terrorists. The cost-benefit ratio is against us! Our cost is billions against the terrorists' costs of millions. It is pretty clear that the coalition can win in Afghanistan and Iraq in one way or another, but it will be a long, hard slog."

Two years after 9/11, the U.S. government's counterterrorism efforts had made great strides. Teams of Special Operations forces and CIA paramilitary officers were coordinating more closely in the field than ever before. The FBI had scored several successes with allied law enforcement agencies, including Pakistani authorities, to kill or capture top Al Qaeda leaders. Treasury Department analysts were cracking terrorists' financial networks. Slowly, barriers to intelligence sharing were crumbling. But two years into the fight, it was dawning on Rumsfeld and Myers at the highest levels of government as well as on people like Jeff Schloesser, Juan Zarate, and Art Cummings on the front lines just how little the U.S. government knew about Al Qaeda and other militant organizations, and how they attracted a growing following in the Muslim world. Bush remained the self-declared "war-on-terror president." But military commanders, senior intelligence officers, and law enforcement officials squared off every day against violent extremists while they also confronted unresolved questions within their own government about competing interests, competing strategies, and a competition for financial resources, personnel, and information. It left many of them wondering who was really in charge of the war on terror.

Copyright © 2011 by Eric Schmitt and Thom Shanker