The Threat Matrix

Inside Robert Mueller's FBI and the War on Global Terror


By Garrett M. Graff

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An intimate look at Robert Mueller, the sixth Director of the FBI, who oversaw the investigation into ties between President Trump’s campaign and Russian officials.

Covering more than 30 years of history, from the 1980s through Obama’s presidency, The Threat Matrix explores the transformation of the FBI from a domestic law enforcement agency, handling bank robberies and local crimes, into an international intelligence agency — with more than 500 agents operating in more than 60 countries overseas — fighting extremist terrorism, cyber crimes, and, for the first time, American suicide bombers.

Based on access to never-before-seen task forces and FBI bases from Budapest, Hungary, to Quantico, Virginia, this book profiles the visionary agents who risked their lives to bring down criminals and terrorists both here in the U.S. and thousands of miles away long before the rest of the country was paying attention to terrorism. Given unprecedented access, thousands of pages of once secret documents, and hundreds of interviews, Garrett M. Graff takes us inside the FBI and its attempt to protect America from the Munich Olympics in 1972 to the attempted Times Square bombing in 2010. It also tells the inside story of the FBI’s behind-the-scenes fights with the CIA, the Department of Justice, and five White Houses over how to combat terrorism, balance civil liberties, and preserve security. The book also offers a never-before-seen intimate look at FBI Director Robert Mueller, the most important director since Hoover himself.

Brilliantly reported and suspensefully told, The Threat Matrix peers into the darkest corners of this secret war and will change your view of the FBI forever.


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Table of Contents


Copyright Page


Public Enemy #1

I shall wage vigorous warfare against the enemies of my country, of its laws, and of its principles…. I shall always be loyal to my duty, my organization, and my country.

—From J. Edgar Hoover's FBI Pledge for Law Enforcement Officers

The final minutes of George W. Bush's eight years as president ticked away as Bob Mueller stepped down onto the inaugural platform. Despite weeks of wall-to-wall news coverage warning of overcrowding for the inauguration—millions of people who might clog the Washington Beltway and the Metro system for hours—the chilly January day had deterred few inaugural-goers. More than perhaps anyone else on the inaugural platform, Mueller, the director of the FBI, was responsible for keeping everyone safe for the day.

The previous twenty-four hours had been nerve-racking, like so many of the days and nights of the past seven years. A threat out of the Middle East, sketchy at best. Reports of a man barreling down the Jersey Turnpike with a bomb. Agents from the FBI, the CIA, and a dozen other agencies fanned across country and several continents, hoping to run down the information before noon Tuesday, H-Hour for the handover of government, democracy's greatest rite—the peaceful and amicable transfer of power from one party to another with nearly diametrically opposed views.

The last time the nation had gathered to do this, in January 2001, the world had been a different place. That was, as everyone now said, before. This was the first transfer of power after. Before, the Clinton administration had balked at targeting a shadowy terrorist named Osama bin Laden in a faraway place called Afghanistan. Before, the argument had been, What had bin Laden ever done to deserve assassination? The United States didn't do that type of thing. Now, after, everything was different.

Just days prior to the inauguration of Barack Obama, Hellfire missiles launched from a Predator drone half a world away from Washington had killed two Kenyans suspected in the 1998 attacks on the U.S. embassies in Tanzania and Kenya. Usama al-Kini, also known as Fahid Mohammed Ally Msalam, and Sheikh Ahmed Salim Swedan likely never saw the missiles closing on them at speeds topping Mach 1.3 and likely never felt the twenty-pound warheads explode. Although the FBI's global footprint had expanded considerably, the United States had no other practical means to eliminate this pair of terrorists. The two men, living in South Waziristan—a remote tribal part of Pakistan most Americans would be hard-pressed to locate on a map—were unreachable. The CIA drones and their Hellfire missiles were a different type of justice, an outside-the-courtroom, permanent justice—one that, after, the U.S. government had decided was more than appropriate to mete out but had been off the table before. (The precise term for such measures—extralegal—had become all too familiar to the American people after.)

Al-Kini and Swedan were both on the Bureau's "Most Wanted Terrorist" list, making the attacks a big victory for the United States, yet, since the United States didn't acknowledge these covert missile strikes, it didn't officially consider them dead. Months later, both men's names would still be on the FBI's public list; inside the government, though, no one was looking too hard for them.

The minutes ticked away on inaugural day. Of the government men onstage, only a few had been in the fateful national security meeting the morning of September 12, 2001, the day after everything had changed. Now, in just two hours, most of them would depart government. A green-and-white Marine helicopter from HMX-1, the presidential helicopter squadron, sat on the East Front Plaza of the Capitol, waiting to ferry George W. Bush back to private life. Vice President Dick Cheney, confined to a wheelchair after straining his back moving boxes the weekend before, would also depart—only to appear in the coming months as a vocal opponent of the new administration's approach to terrorism. Of the entire national security team, those departures would leave only Mueller still in the position he had held on September 11, 2001, that brilliant and crisp fall day when the planes had come.

Only one other member of the national security team would be carrying over from Bush to Obama—and his absence today was intentional. Hidden in a secure location outside Washington, Robert Gates—the wizened secretary of defense who on 9/11 had been a dean at Texas A&M—was, in the bland parlance of bureaucracy, the "designated successor," part of the elaborate continuity-of-government plans created during the Cold War to ensure the United States would survive even the most catastrophic assault. Originally designed to protect against surprise Soviet intercontinental ballistic missiles coming in over the North Pole, the continuity-of-government operation now mostly guarded against terrorists with a smuggled nuclear weapon stuffed in a suitcase. In the coming hours, a new national security team would begin to flow into the federal apparatus across the city and move into the White House, where air pressure is always kept elevated to ensure biological or chemical agents can't penetrate inside. Only Mueller would be left among the security team to recall the fear, tension, and shock of September 12, 2001, the uncertainty of the day after. The soldiers in the streets; the smoke, visible from his office, rising from the Pentagon across the Potomac River; the concrete barriers that sprang up everywhere overnight like some sort of ugly, aggressive species of weed; that smell—part burning jet fuel, part burning paper, part burning flesh.

Mueller, wrapped in long overcoat and scarf, his gloved hands protected from the cold, walked to the front of the stage, his longtime wife and companion, Ann, by his side. On 9/11, just days after moving to Washington, she had sat through that historic day alone, watching the television in their temporary apartment six blocks from where they now stood. Her husband hadn't returned until long after she'd gone to sleep.

From the banister, they could survey the largest crowd ever assembled for a presidential inauguration. It spread out for over a mile, the length of the National Mall, the nation's so-called backyard. Somewhere out in the crowd were 155 teams of Mueller's agents in plainclothes, watching for anything unusual. A few blocks away, the FBI Hostage Rescue Team, created thirty years earlier as the nation's elite antiterror strike force, sat poised to react. To back them up, SWAT teams, hazardous-material units, bomb squads, and even weapons of mass destruction response teams were located at strategic points around the crowded city. Armored military-like vehicles topped with flashing lights were hidden just out of sight, ready for action. Police helicopters circled the city, their expensive sensors and surveillance gear hard at work. Gas masks hung from the waists of thousands of law enforcement personnel, as well as the National Guard troops who stood on every street corner for miles. Fighter jets bristling with missiles slung under their wings waited to respond to trouble from above, while deep beneath the city Secret Service agents searched tunnels and sewers for trouble below. Most military coups in the world were carried out with less firepower, materiel, and personnel than were deployed to the streets of Washington for what everyone hoped would be a peaceful and uneventful transition of power.

The early-morning crowd before Mueller was ecstatic despite the hour, the security hassles, and the bone-chilling cold. While the crowd on the Mall and in the Capitol complex was swept up in the euphoric moment of hope and the promise of change brought about by the election of the nation's first black president and a team representing a youthful new generation of leadership, Mueller knew the fear that prevailed behind the scenes.

Until hours earlier, it had seemed possible that the day would go very differently. Three different threads of intelligence had indicated that al-Shabaab, one of the many Islamic jihadist groups that formed the international web of al-Qaeda affiliates, had dispatched attackers from its base in Somalia to slip across the Canadian border and explode bombs on the Mall during the inauguration. The government had been tracking the intelligence for weeks, but only recently had new information moved the threat onto a different tier of seriousness.

Harakat al-Shabaab al-Mujahideen—the "Movement of Warrior Youth"—was still relatively new to the terrorism game; it wouldn't even formally be declared a "Foreign Terrorist Organization" by the State Department for another month, yet its capabilities were already well-known enough to seriously worry the government officials in the days leading up to the inauguration. (Kenya, the president's ancestral country and the site of the 1998 embassy attack that had helped usher in the age of al-Qaeda, was also under threat, according to the available intelligence.)

The national security teams of President Bush and President-elect Obama had been gathering repeatedly in the White House and at the guest residence, Blair House, for the week leading up to the inauguration to track the latest intelligence. The rooms pulsed with a sense of nervous energy on the part of the new Obama staff and a world-weariness on the part of the Bush officials who had only days left to go in their public service.

While the two national security teams didn't have much history working together, sitting on one side was a face familiar to everyone: John Brennan, one of the nation's most skilled counterterrorism leaders who had led the newly formed National Counterterrorism Center after 9/11, only to part ways with the Bush administration over its handling of the Iraq war. Brennan had become a close adviser to the Democratic nominee and had been the top candidate to take over the CIA until concerns about his role in the Agency's enhanced-interrogation program earlier in the decade had forced him into a position that didn't require Senate confirmation. Now Brennan served as the calming force on the Obama team in the room. He'd been through this sort of thing before.

A week before, the two national security teams had teased out a mock scenario imagining multiple bombs detonating simultaneously around the country—a domestic version of what had happened in East Africa in 1998, in Madrid in 2004, and twice in London in 2005. Hanging over every meeting and every discussion was a question spoken only in whispers: How real did the threat have to be before the government should consider canceling the ceremony or moving it indoors to a secure location? There was some precedent: President Reagan's second inaugural had been moved to the Capitol Rotunda because of nasty cold weather. This weather was heavier.

In one meeting, incoming secretary of state Hillary Clinton had asked a pointed question: "So what should Barack Obama do if he's in the middle of his Inaugural Address and a bomb goes off way in the back of the crowd on the Mall? What does he do? Is the Secret Service going to whisk him off the podium, so the American people see their incoming president disappear in the middle of the Inaugural Address? I don't think so." But was that truly credible?

The decision was made: Obama would continue the speech, if at all possible.

Nearly every passing hour brought new information. One terrorist suspect was chased through Heathrow Airport—British police officers literally running, their radios and utility belts banging against their hips as they charged through the heavy crowds—only, after further investigation, to be deemed harmless, a false alarm. An interrogation team in Uganda was calling Washington regularly as one source was hooked up to a polygraph machine to test his trustworthiness. The U.S. polygrapher was under intense pressure: Is this guy legit? Are you sure? The inauguration could hang on the answer.

On inauguration eve, the president-elect had canceled the final run-through of his Inaugural Address to go over the latest intelligence one more time at Blair House. His aides could tell the pressure was weighing on him. Since just after the election, he'd been getting the presidential daily threat briefings from the CIA and the rest of the U.S. security apparatus. After one pre-election briefing by Director of National Intelligence Mike McConnell, then-Senator Obama had said wryly, "You know, I've been worried about losing this election. After talking to you guys, I'm worried about winning the election." Now, with the heavy crown poised to rest on his head, each day seemed to bring new threats and causes of concern for President-elect Obama.

The Inauguration Day threat provided a key lesson for the new administration: No matter what else President Obama hoped to accomplish during his tenure in office, no matter if the most pressing issue seemed to be an economy teetering on the brink of complete collapse, no matter if he hoped to pass a game-changing health care bill in his first year in office, or if he hoped to change the nation's direction by closing the Guantánamo Bay prison and withdrawing troops from Iraq and Afghanistan, he didn't get to dictate when and where the terrorists engaged. Al-Qaeda and its affiliates might have been on the defensive, but the advantage on the field was still theirs. The government, after all, had set itself a standard of being successful in stopping attacks 100 percent of the time. The bad guys only had to get lucky once.

The next morning, the soon-to-be leader of the free world had marked the day by attending the traditional service at St. John's Church. Bishop T. D. Jakes read from the Book of Daniel, explaining, "In times of crisis, good men must stand up. God always sends the best men into the worst times." Across the street, the two national security teams huddled for a final round of meetings. For Mueller, it would be the last time he sat in conference with many of the colleagues he'd spent years working alongside. Condoleezza Rice had been in that meeting the day after. Mike Hayden, only hours left in his tenure as CIA director, had been head of the National Security Agency on 9/11. Attorney General Michael Mukasey had been a federal judge in New York, where he'd helped set major legal precedents in the unfolding war on terror. Then there were the new folks, including one man who made the normally stoic Mueller smile: Eric Holder, the incoming attorney general, was one of his longtime colleagues; the two men had been prosecutors in the District of Columbia a decade before.

The joint meeting, poignant for many in the room, had left everyone feeling more at ease. After all the worry, the al-Shabaab threat was amounting to nothing. Before it had even taken office, the Obama administration had survived its first false alarm; for the outgoing Bush administration, the fizzled plot was the last of thousands of such false alarms since that morning in September 2001.

On that day, Barack Obama had been an Illinois state senator, evacuating the Illinois legislative offices as ordered during the moments when everyone believed everything and everywhere was a target. Years later, he had run for president partly on a platform of ending the most morally troubling aspects of his predecessor's approach to terror. "It's time to turn the page," he'd said in one 2007 speech. Now, as the president-elect climbed into his new limo, the reminders of the era after literally surrounded him—his new ride, nicknamed "the Beast," was a freshly upgraded version of the presidential limo custom-built by GM that could withstand rocket attacks, seal off the interior from outside air, and deploy tear gas. The man who would soon pledge to "the best of my ability, preserve, protect, and defend the Constitution of the United States" would redefine in the coming years his own fight in the age of global terror. His first executive orders after being sworn in—documents that were already drafted and prepared for his signature as he rode down Pennsylvania Avenue toward the Capitol—banned torture in interrogations and committed to closing the Guantánamo Bay prison within a year (a deadline that would slip and later be almost abandoned entirely).

As Obama reclined in "the Beast," flipping through papers while passing the crowds lining the streets, Mueller looked over the crowd on the Mall. The FBI director was confident—or at least as confident as one could be these days—that the event would proceed as scheduled. Yet the huge behind-the-scenes security apparatus still churned away. The al-Shabaab threat might have been averted, but there were all sorts of other things to worry about.

Eight blocks from the Mall, in the FBI's Washington Field Office (WFO in Bureau parlance), more than a hundred agents and representatives from other agencies monitored the inaugural scene by remote camera in the top-floor Command and Tactical Operations Center (CTOC). Down the hall, a team of linguists listened to live SIGINT intercepts—that is, signals intelligence, like phone taps—for any sign of trouble. The WFO command center featured scores of workstations, each tasked with a specific role, spread out in a room packed with computers, ringing telephones, and giant wall screens. One projector screen scrolled live intelligence combed from all of the assembled agencies. Maps showed the location of countersniper teams around the event and the parade route. Every possibility had been gamed out, every response calculated. Across the street from the Washington Field Office, the Secret Service was working to secure the National Building Museum, the site of one of the more than a dozen inaugural balls set for that evening. It would be a long day.

Luckily for Mueller, as the moment of handover neared, he was confident in the Bureau's knowledge, planning, and response, and he was able to worry about other things. At 10:32 A.M., with eighty-eight minutes to go until the reign of George W. Bush entered the history books, he wanted to know: "Where's Melissa?" Somewhere in the million-person crowd below were his daughter and her boyfriend, fresh in from New York. Even with the most sophisticated surveillance gear ever assembled in American history for this event, some things would remain a mystery.

For almost five years after 9/11, Bob Mueller and the attorney general—first John Ashcroft, later Alberto Gonzales—met every morning in the FBI's Strategic Information and Operations Center (SIOC, pronounced "sigh-awk," in FBI jargon) and then shortly after 8 A.M., piled into their armored Suburbans in the basement of the Hoover Building for the short run up Pennsylvania Avenue to the White House. Weaving at high speed through the barriers around the executive complex, the motorcade, bristling with tense, heavily armed agents, would pull up just outside the West Wing. They carried with them a copy of the day's "Threat Matrix," a printed spreadsheet of all the various terrorist plots and worrisome intelligence the government was currently tracking. At 8:30, the duo, joined by a few aides, would be ushered into the Oval Office to update the president on the Threat Matrix just as the CIA was wrapping up its morning intelligence briefing. Trying to lighten the tension on one of those scary early days, President Bush, an avid sports fan, summarized the 8 A.M. CIA briefing and the following 8:30 FBI briefing as "first offense, then defense." He was basically right.

Since J. Edgar Hoover took over the Bureau in the late 1920s, the FBI had led the nation's defense, blocking and tackling an ever-evolving set of criminals and evildoers who sought to harm the United States. For seven decades, we have turned to the FBI to protect us from that which we fear the most. The forms our fears have taken have dictated their ever-changing set of priorities, requiring a constantly changing set of skills and specialties.

The sheer breadth of what is forced onto the FBI's plate each year is staggering. In the summer of 2008, the FBI investigated claims of an NBA referee that the basketball playoffs were rigged. That fall, as the economy collapsed under a wave of bad mortgages, the FBI launched mortgage fraud task forces across the country, building off the financial expertise it developed earlier in the decade when it was called upon to investigate the string of collapses of Enron, Global Crossing, and other corporate whirlpools. The threat of Somali pirates meant agents were off to the Horn of Africa. All the while, they investigated some hundred thousand other crimes, ranging from bank robberies to kidnappings to corrupt public officials, and worked to keep foreign spies from stealing our secrets. That's more or less how we want it. We expect that the morning after something bad happens—whatever it is, whatever American value is threatened—the news headlines will begin "FBI launches investigation into X," or "FBI arrives on scene of Y." Everything will be okay, we're told; the FBI is here. when Congresswoman Gabrielle Giffords was shot in January 2011, President Obama underscored his concern by immediately dispatching Mueller to Tucson to head the investigation personally.

That belief that the FBI is all that stands between decent, hardworking, law-abiding, taxpaying Americans and those who seek to do us harm was precisely the construct J. Edgar Hoover worked fanatically to create for half a century. As Hoover biographer Richard Gid Powers once explained, "Because of [Hoover's] success in turning the FBI into a symbol of justice, the public had come to expect the dispatch of FBI agents as an indication of the concern of the Federal Government."

In 1924, Hoover had been handed control of the Bureau, a corrupt investigatory backwater used by the government for whatever purposes suited it; the 441 agents were mostly political cronies or investigators who had washed out of jobs elsewhere. They had little power and even less respect. Hoover was a progressive of the first rank. With the backing of the attorney general, Harlan Fiske Stone, he changed promotion rules, fired or sidelined the worst of the political patrons, and instituted a formal training program. As his efforts succeeded, the quality of the Bureau began to rise—although he still needed something dramatic to prove that to the country.

He found it at Union Station in Kansas City, Missouri, the "Gateway to the West."

The FBI's myth starts with the capture of a notorious escaped convict named Frank Nash, in Hot Springs, Arkansas, a dangerous organized crime center during the 1930s. Because FBI agents didn't yet have the power to arrest people or carry firearms, the Bureau had taken a local police chief along with them to make Nash's capture marginally legal.* Then came the challenge of getting Nash five hundred miles back to Leavenworth Penitentiary in Kansas while staying one step ahead of the friends who would seek to rescue Nash before he was safely locked up again. After a hair-raising high-speed escape from Hot Springs by car, during which the two agents and the police chief talked their way through two roadblocks set up by corrupt Arkansas police set on freeing Nash, the team boarded the overnight train to Kansas City and hunkered down in a cabin to wait.

The cavernous Union Station in Kansas City was one of the busiest train stations in the country during its heyday in the teens and twenties. On some days more than 250 trains rolled through the station. Even at 7 A.M. on the Saturday morning of June 17, 1933, the station was busy—a half-dozen trains were due in that hour alone. The Travelers Aid station was just opening in the T-shaped main hall as two Kansas City police officers and two local FBI agents pulled up and parked illegally outside the east doors. They hurried down to the tracks, meeting the overnight Missouri Pacific train from Arkansas as it pulled up.

After hearing a prearranged knock on their cabin door, the nervous lawmen emerged with their prisoner. They knew trouble was possible and had arranged to drive him the last leg rather than wait the hour for the train to continue north on to Leavenworth Penitentiary. There was no time to waste—in this region, at this time in history, Nash had more friends around than the FBI did.

Witnesses would later vividly recall the flying wedge of lawmen that sliced through the morning travelers, escorting Nash through the hall toward the curb. The group was just settling Nash into the front seat of the FBI's Chevrolet when a group of gunmen emerged out of the bustling crowd on the curb and ambushed them.

As the story goes, a gangster appeared brandishing a machine gun and shouted, "Up, up!" Then another gunman yelled, "Let 'em have it!" In the Bureau's official retelling of the story, lead ripped into the police cars from nearly every direction as three (or perhaps four or maybe it was seven) gunmen slaughtered the group of Bureau agents and Kansas City lawmen. Machine gun bullets riddled the front of Union Station—some scars of which are still visible today in the granite facade. When the smoke cleared, the two Kansas City policemen who had met the group at the station were dead, as was the police chief who had accompanied the FBI agents to Arkansas to capture Nash. One Bureau agent was killed, two other agents were wounded; only one agent escaped harm. And, most recklessly, as the Bureau's official history concludes, "The prisoner, Frank Nash, was also killed by a misdirected gunshot that entered his skull, thereby defeating the very purpose of the conspiracy to gain his freedom."

The horror of the scene was quickly telegraphed to Washington and from coast to coast. Hoover immediately ordered every Bureau resource available to hunt for the killers who had embarrassed his fledgling agency. In the coming weeks, the FBI would track down and capture or kill in the process all three men they believed responsible for the rampage: bank robber and Nash friend Verne Miller, notorious killer Charles "Pretty Boy" Floyd, and Floyd's sidekick, Adam Richetti.

The bloody shootout at Union Station forever changed the American public's perception of crime. The senseless and immoral slaughter of the supposedly unarmed public servants in full view of the Kansas City public was an outrage to the rule of law, the nation, and American values. While colorful bank-robbing gangsters had been the toast of the country in the midst of the Depression, the Kansas City Massacre instantly united public opinion against them. Within a year, Hoover had used the incident to justify nine strict anticrime laws that professionalized the Bureau—granting it rights to arrest suspects anywhere in the country, to execute warrants, and to carry firearms—and federalizing crimes including transporting stolen goods or fleeing across state lines, robbing banks, and killing or injuring federal agents. Thanks to the events of that Saturday morning in June, the FBI would have the power to search the country for criminals and bring them to heel. A national police force had been born, Hoover was its head, and—as the Kansas City investigation would prove—it always got its man.

Or so goes the myth. The reality of the Kansas City Massacre bears little resemblance to the story sold to the public. True, friends of Frank Nash certainly did try to free him from the Bureau outside Union Station. True, four lawmen died needlessly in the Kansas City dawn. The rest is fiction.


  • Kirkus Reviews: One of the best nonfiction books of 2011.

    "Action-filled, richly detailed portrait of the Federal Bureau of Investigation in its new guise--charged not just with solving crimes already committed, but now with preventing at least some of them...There's solid storytelling at work here--and quite a story to tell, too."—Kirkus Reviews, starred review
  • "The Threat Matrix is...a well-told story and a reading pleasure."—The CIA journal Studies in Intelligence (September 2011)

On Sale
Mar 28, 2011
Page Count
704 pages

Garrett M. Graff

About the Author

Garrett Graff is the editor-in-chief of The Washingtonian. He is the author of The First Campaign: Globalization, the Web, and the Race for the White House (FSG, 2007) and the founding editor of the, the first blog to cover the White House press briefings.

Learn more about this author