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The FBI’s highest-ranking Arabic-speaking agent is a ghost. He goes to work each day, but walks the halls like an empty suit. Fellow agents whisper about his loyalty and talk about throwing him “off the roof.” Bassem Youssef, after all, is the whistleblower at the center of two of the FBI’s biggest ongoing scandals: its rampant abuse of national security letters to access confidential information on US citizens, and its failure to recruit Arabic-speaking agents. He’s sued the bureau for discrimination and has been sidelined to a paper-pushing job. Yet he won’t quit—he remains determined, he says, to fight the war on terror, even if he has to battle his bosses to do it.

It wasn’t always so. In the mid-1990s, if you were to call the FBI and ask for Bassem Youssef, the switchboard operator would tell you there was no such person. Known in those days by his alias, Adam Shoukry, Youssef was a star counterterrorism specialist, one of only a few agents in bureau history whose work was deemed so sensitive that the attorney general allowed him to go undercover within the FBI itself. Almost a full decade before the 9/11 attacks, he managed to penetrate “Blind Sheikh” Omar Abdel-Rahman’s Islamic Group, which carried out the 1993 World Trade Center bombing. (Some of its key members later joined Al Qaeda, which Youssef identified as a threat long before it was on most intelligence agents’ radar.) The details of Youssef’s service during this period remain classified, but his value as an agent was such that, in November 1994, he received the Director of Central Intelligence Award, a high honor reserved for the intelligence community’s most skilled operators.

But after 9/11 Youssef’s once-rising star came crashing down. He charges that he was suddenly bypassed for counterterrorism assignments because of his ethnicity, a fate emblematic of a larger problem with the bureau’s approach to counterterrorism. Since 2001, the FBI’s budget has grown 114 percent, from $3.3 billion to $7.1 billion in fiscal year 2009; today, its 12,000 special agents include just 57 with even rudimentary knowledge of Arabic. Only six—including Youssef—were rated “advanced professional” in the language as of 2006. By comparison, the New York Police Department has more than 60 Arabic-speaking cops. The FBI’s failure, Youssef says, is a result of deeply rooted institutional discrimination against Middle Easterners—a population the bureau should be recruiting in droves, but instead has largely shut out.

Though a pariah to his fellow agents, Youssef remains a senior FBI official with a top-level security clearance. I spent nearly a year trying to gain an interview with him; when the FBI finally gave permission, it came with the requirement that Youssef’s lawyer be present to ensure that the conversation did not stray into sensitive areas. (The bureau itself declined to comment about his case.)

We met on a cold, overcast day at the Georgetown office of Stephen Kohn, one of Washington’s leading whistleblower advocates (and Linda Tripp’s one-time attorney). Youssef arrived looking every bit the G-man stereotype: dark suit, black tie, starched white shirt. Slight of frame, with close-cropped, charcoal-gray hair and brown eyes, he was easygoing and quick to smile, though his bitterness occasionally showed through. On the way to a nearby restaurant, we joked about the public-relations obstacle course I’d overcome to get permission to meet him.

Born in Cairo in 1958 to parents who were both accountants, Youssef grew up in an affluent neighborhood and studied at an English-language prep school. In 1972, when he was 13, the family relocated to Southern California, where Youssef quickly embraced everything American. He went on to attend California State University-Los Angeles, but his dream was to fly F-14 Tomcats. (Top Gun had just come out.) He made it through the initial rounds of pilot testing, and even had his head measured for a flight helmet, but ultimately failed on account of his mild colorblindness. (He couldn’t distinguish a shade of green displayed on fighter-plane instrument panels.) Youssef sulked for a couple of months before taking a friend’s advice to meet with a local FBI recruiter. A year and a half later, having passed an exhaustive series of background checks, he moved to Virginia.

Youssef became a hot commodity at the bureau, where he single-handedly doubled the number of native Arabic speakers. In 1988, right after graduating from the training academy at Quantico, he was assigned to St. Louis, where he joined a small team of agents hunting US-based associates of Abu Nidal, the leader of a Palestinian extremist group. It was a heady time for the young agent; he cut his teeth doing surveillance, making arrests, and conducting interrogations in Arabic.

As his reputation spread, Youssef says, agents in other field offices and at FBI headquarters frequently approached him for advice on their own cases. Before long, he transferred to the Los Angeles field office, where, for security, he assumed the identity of Adam Shoukry.

It was in L.A. that Youssef achieved a major intelligence coup. He had tried to obtain a wiretap on a terrorist cell associated with the Islamic Group weeks before the 1993 World Trade Center attack. After the bombing, Youssef and his supervisors set up an intelligence-gathering operation to reach inside Abdel-Rahman’s organization. “It’s a very, very difficult group to penetrate,” says one of Youssef’s former supervisors, Edward Curran, a 38-year FBI veteran who is now deputy director of New Jersey’s Office of Counter-Terrorism. “[Youssef] did it. He did it day and night. He was out on the street, was taking opportunities…He knew how to exploit them more than any other person in the office.” The specifics of Youssef’s work have never been made public, but court documents suggest that by flipping one of Abdel-Rahman’s key associates, Youssef puzzled together much of the Islamic Group’s membership. “You can’t even begin to describe it,” says Curran. “Bassem was the counterterrorism program. He was the entire program.”

It was no surprise when Youssef became the FBI’s legal attaché to Saudi Arabia in February 1997. The previous summer, a high-rise apartment complex called the Khobar Towers, home to about 2,000 US military personnel stationed at King Abdul Aziz Air Base, had been torn apart by a truck bomb, killing 19 and injuring 372. Historically, the Saudis had been reluctant to cooperate with US investigators, sometimes beheading suspects before they could be interrogated. But Youssef’s knowledge of the culture quickly ingratiated him to his Saudi counterparts, who enjoyed teaching the FBI man the subtleties of Saudi slang. Within three months of his arrival, according to an FBI report drafted in 2000, Youssef’s “efforts led to the establishment of direct communications with senior officials of the Mahabith [Saudi Arabia’s security service] which had previously been unavailable to US Embassy personnel.” These contacts helped pave the way for a first-ever meeting between then-FBI director Louis Freeh and top Saudi officials, after which the FBI was given access to all six Khobar bombing suspects.

Youssef, though, had moved on to another target: He was increasingly troubled by the growing threat posed by Al Qaeda and, according to the report, became “preoccupied with Bin Laden’s current status and whereabouts.” In 2000, after four years in Riyadh, he was given a post at the National Counterintelligence Center, an interagency task force housed at the CIA’s Virginia headquarters. But in April 2001, program restructuring eliminated his position. He was still waiting for reassignment on September 11, 2001.

After 9/11, the bureau—mortified by its failure to pick up the attackers’ trail despite multiple opportunities—went into overdrive. It pulled hundreds of agents from its criminal division, even rookies from Quantico, into counterterrorism work. Youssef’s phone, though, never rang. When he finally got his new assignment in March 2002, he was sent to the Document Exploitation Unit, a team of low-level agents tasked with reviewing evidence recovered in Afghanistan and elsewhere. A lower-ranking agent with no counterterrorism pedigree became his supervisor. Stunned, Youssef called his congressman, Rep. Frank Wolf (R-Va.), for help.

On June 28, 2002, FBI director Robert Mueller was called to a meeting in Wolf’s office; he found Youssef waiting for him. The agent explained that he had tried hard to find a counterterrorism assignment through the appropriate channels, but now felt he had no recourse but to approach the director personally. Mueller said he’d look into the matter and assured Youssef that he would suffer no retaliation.

For a year, nothing happened. Finally, in July 2003, Youssef gave up hope and filed suit for discrimination.

As it turned out, the meeting with Mueller had sealed his fate. Unbeknownst to Youssef, two days earlier Mueller had signed off on his request for a transfer to the International Terrorism Operations Section, the FBI’s lead unit in the fight against Al Qaeda. But the director seemed to have had a change of heart. The transfer never came through, and Youssef didn’t learn of Mueller’s move until years later.

Youssef’s meeting with Mueller also appears to have ignited a whisper campaign about his loyalty. According to an affidavit filed by one FBI agent, Youssef’s colleagues gossiped that he was a Muslim (he’s actually a devout Christian), that he “had refused to carry out orders…because of his religious faith,” and that his time in Saudi Arabia had been an embarrassment to the bureau. None of this was true, but similar allegations dogged the two agents who replaced Youssef in Riyadh: an Egyptian Muslim who was accused of refusing to wear a wire, and an American convert who had been Youssef’s assistant and previously worked airport security for the bureau.

Much of Youssef’s trouble securing a position after 9/11 may have stemmed also from the FBI’s astonishing claim that neither fluency in Arabic nor knowledge of the Middle East is necessary for leadership positions in the counterterrorism division. As Gary Bald, a former top FBI counterterrorism official, told Youssef’s lawyer, Stephen Kohn, in a deposition, “You need leadership. You don’t need subject-matter expertise. It is certainly not what I look for in selecting an official for a position.”

Others in the intelligence community scoff at such claims. “Knowing about counterterrorism (say, for example, that most Al Qaeda operatives have a logistics team that prepares the way for them) would help a supervisor ensure a proper investigation and avoid missing important aspects of the case,” wrote former CIA analyst Dan Byman in support of Youssef’s suit. Michael German, a counterterrorism agent who quit the bureau in 2004 after blowing the whistle on his superiors for illegal wiretapping, described the FBI’s position as “indefensible” and “ridiculous.” He told me, “You wouldn’t hire somebody to remodel your kitchen who didn’t know anything about remodeling a kitchen.”

Today, Youssef ostensibly heads up the Communications Analysis Unit, charged with processing bureau requests to private telecommunications firms for access to client records. It’s a job in which “my language, my background, my operational experience, [and] my liaison experience…are not utilized at all,” he says. “I’m at a point now where I’m not even utilized in the decision making within my own unit. Bosses will go right to my subordinates.”

But if bureau executives thought that relegating Youssef to a desk job would keep him quiet, they were in for a disappointment. Shortly after Youssef took over as CAU unit chief in early 2005, he noticed widespread irregularities in the FBI’s use of national security letters, a kind of administrative subpoena demanding customer information from private companies. After 9/11, the number of NSLs exploded, rising from 8,500 in 2000 to 143,000 between 2003 and 2005. Many were sent without any evidence linking them to ongoing counterterrorism investigations. The bureau also sent out hundreds of “exigent letters” demanding immediate access to telephone companies’ client records without an official subpoena.

Youssef notified his supervisors of the scope of the problem. For months, they did nothing. Finally, in September 2005, the bureau’s general counsel’s office called a meeting. According to staffers for Sen. Chuck Grassley (R-Iowa), who has pressed for answers on why Youssef was sidelined so abruptly, FBI lawyers initially focused not on eliminating the abuse but on devising a legal work-around: the opening of a series of large, vaguely defined investigative files that could be used to gain access to the private records of US citizens. Youssef used his position at the CAU to block the plan. The following year, after word of the abuses leaked, Department of Justice inspector general Glenn Fine opened an official inquiry. Youssef became a material witness in the case and gave several days’ worth of testimony, which made him even more unpopular with his colleagues. Youssef says one agent Fine interviewed later boasted that he “threw Youssef under the bus.” Another agent was overheard asking a colleague if he was “getting ready to throw Bassem Youssef off the roof.”

Historically, in its dealings with whistleblowers like Youssef, the bureau’s instinct has been to go on the attack. “The Youssef case captures the cultural problem at the FBI,” says Sen. Grassley. “It’s an example of higher-ups and the bureaucracy spending a lot of energy and resources to kill the messenger.”

Youssef knows there’s little chance of resurrecting his career. He stays on at the bureau in the hope of changing the culture by example—though that may be unlikely under Mueller, whom Obama has retained as director. The counterterrorism division, he says, is no better prepared today than it was before 9/11, and might even be worse off. He invoked a M*A*S*H metaphor: “There’s an episode where Colonel Potter’s horse ran away. B.J. Hunnicutt and Hawkeye go looking for it. They don’t know a thing about horses. Hawkeye’s got this lasso, and he says, ‘Anybody know anything about horses?’ And his partner, B.J., says, ‘I stepped into some horse manure once!’ Hawkeye says, ‘You’re in charge.’ That’s the state of affairs in the counterterrorism division of the FBI.”