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This article was originally published by ProPublica, a Pulitzer Prize-winning investigative newsroom.

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From the first weeks after the 9/11 attacks, suspicions about a possible Saudi government role in the plot have focused on a mysterious, 42-year-old graduate student who welcomed the first two Al-Qaeda hijackers after they landed in Los Angeles in January 2000.

The Saudi student, Omar al-Bayoumi, claimed to have met the two terrorists entirely by chance; he said he was just being hospitable when he helped them settle in San Diego. Both the FBI and the 9/11 Commission supported Bayoumi’s account, dismissing the suspicions of agents who thought he might be a Saudi spy.

After nearly 20 years, however, the FBI has changed its story. In documents declassified last year, the bureau affirmed that Bayoumi was in fact an agent of the Saudi intelligence service who worked with Saudi religious officials and reported to the kingdom’s powerful ambassador in Washington.

Those revelations have now become a central point of contention in a long-running federal lawsuit in New York, where 9/11 survivors and relatives of the 2,977 people who were killed are seeking to hold the Saudi government responsible for the attacks.

Lawyers for the families argue that the new evidence so contradicts earlier Saudi claims that they should be allowed to seek new information from the country’s intelligence service about Bayoumi and another official who reportedly aided the hijackers, Fahad al-Thumairy.

“Saudi Arabia has a duty to tell the truth about the intelligence roles of Bayoumi and Thumairy based on its actual, complete knowledge,” the plaintiffs wrote in a motion this month.

The federal magistrate who is managing discovery in the case, Sarah Netburn, has so far sided with the Saudis, finding “no compelling reason” to reopen the document search or order new interviews with Saudi officials. The families’ lawyers have asked the judge overseeing the case, George B. Daniels, to overrule her.

The Saudi government has always denied playing any role in the 9/11 attacks. A joint CIA-FBI report in 2005 concluded there was “no evidence” that the Saudi government or royal family “knowingly provided support” for the 9/11 plot. It also claimed there was “no information” that Bayoumi was a Saudi “intelligence officer” or that he “wittingly” aided the hijackers.

Regardless of the impact that the Bayoumi information might have on the litigation, it has already rewritten an important part of the story about how the Qaeda plotters took their first, incongruous steps in Southern California.

The chief architect of the attacks, Khalid Shaikh Mohammed, is said to have denied that the hijackers had any confederates waiting for them in the United States. After being tortured by his CIA captors, Mohammed told them he instructed the first two hijackers to present themselves at local mosques as newly arrived students seeking help, the 9/11 Commission stated.

The two Saudis, Khalid al-Mihdhar and Nawaf al-Hazmi, were known to both Saudi intelligence and the CIA as Qaeda operatives. The CIA was watching as they joined a Qaeda planning meeting in Kuala Lumpur, Malaysia, in the first days of January 2000. But the agency said it lost track of the two when they flew on to Bangkok and then to Los Angeles on Jan. 15, 2000. The CIA did not alert the FBI for more than a year after it learned the terrorists had entered the United States using their real names and Saudi passports.

Mihdhar and Hazmi, who were both in their mid-20s, were notably ill-equipped to make their way in the West. They spoke almost no English and understood little about American culture. When they tried to take flight lessons in San Diego, their instructor quickly gave up on them because their language skills were so poor.

For years after the attacks, FBI investigators were uncertain how the two hijackers spent their first two weeks in Los Angeles. But later evidence suggests they arrived almost immediately at the King Fahad Mosque in Culver City, just down the street from Sony Pictures Studios.

The white-marble mosque was an anchor of a Saudi government network of religious operatives who propagated the kingdom’s conservative Wahhabi faith around the United States. Some clerics and others in the network also worked with the Saudi intelligence service, reporting on Muslim communities and keeping an eye on dissident Saudis overseas.

“Saudi government officials and intelligence officers were directly operating and supporting the entities involved with this network,” the FBI stated in a lengthy 2021 synthesis of reporting on the Saudi connections that was declassified last year.

The FBI’s initial investigation of the 9/11 plot focused in part on Thumairy, a 32-year-old cleric who served the religious network as an imam at the King Fahad Mosque while also credentialed as a midlevel diplomat at the nearby Saudi Consulate.

In 2007, the FBI began a follow-on inquiry, Operation Encore, which delved more deeply into the mosque’s ties to the hijackers. One witness, vetted by both the FBI and CIA, told Encore investigators that Thumairy asked a trusted parishioner, Mohammed Johar, to house the two Saudis after they arrived in Los Angeles. The informant said Johar was also told to take the hijackers to the small halal cafe where they met Bayoumi on Feb. 1. (In interviews with ProPublica, Johar minimized his help for the two men and denied that it came at Thumairy’s request.)

Although FBI witnesses suggested that Bayoumi received instructions at the consulate to go to the cafe, he claimed he just happened to stop there for lunch and introduced himself after he heard Hazmi and Mihdhar speaking Gulf-accented Arabic.

Bayoumi said he suggested that his compatriots move to San Diego, which they did three days later. He arranged for them to rent an apartment in his building, set up a bank account for them and briefly lent them $1,558 for their rent and security deposit. He also introduced them to various Muslim immigrants who helped them with tasks like setting up personal computers, starting English classes and getting driver’s licenses.

The FBI office in San Diego, suspicious of Bayoumi’s ties to local Muslim extremists, had begun a preliminary investigation of his activities in 1998. Rather than attend graduate school, agents found, Bayoumi frequented local mosques, doling out money for various causes and frequently videotaping visitors in an unsubtle way. He reportedly put up $400,000 to start a mosque in the San Diego suburb of El Cajon. Throughout his time in the United States, Bayoumi was paid a stipend and other expenses as a ghost employee of a Saudi contracting company, the FBI reported.

Nonetheless, an FBI official, Jacqueline Maguire, testified to the 9/11 Commission in 2004 that Bayoumi’s initial meeting with the hijackers appeared to be “a random encounter.” The commission, which interviewed Bayoumi in Saudi Arabia, judged him a devout, outgoing man and accepted his denials that he was a spy.

More than a decade later, Maguire repeated to a 9/11 review commission that Bayoumi’s dealings with the hijackers appeared to be “accidental.” The Encore investigators strongly disagreed, but their small team was disbanded in 2016 by senior FBI officials in New York.

A more definitive FBI report that was declassified last year validates the Encore agents’ suspicions. That document, dated June 14, 2017, states that from 1998 until the 9/11 attacks, Bayoumi “was paid a monthly stipend as a co-optee of the Saudi General Intelligence Presidency (GIP) via then Ambassador Prince Bandar bin Sultan Alsaud.” In the lexicon of intelligence gathering, a co-optee is generally a diplomat or other official who is recruited by their government’s spy service for a specific task or mission, usually of lesser importance.

The information that Bayoumi gathered “on persons of interest in the Saudi community in Los Angeles and San Diego and other issues, which met certain GIP intelligence requirements, would be forwarded to Bandar,” the FBI report says. “Bandar would then inform the GIP of items of interest to the GIP for further investigation/vetting or follow up.

“Allegations of Albayoumi’s involvement with Saudi intelligence were not confirmed at the time of the 9/11 Commission Report,” the report notes. “The above information confirms these allegations.”

Another FBI report, dated the following day, cites “recent source information” as confirming Bayoumi’s work for Saudi intelligence services.

“We could see from a block away that Bayoumi was an intelligence guy,” the lead agent on the Encore team, Daniel Gonzalez, said in an interview. “It’s evident now that he was tasked with helping the hijackers — that he was running a clandestine operation. So, who was running it?”

The FBI documents do not clearly answer that question. But they add detail to an existing picture of calls and meetings among Bayoumi, Thumairy and members of the Saudi government’s religious network around the time of the hijackers’ arrival in California.

Just before meeting with the hijackers, Bayoumi met at the Saudi Consulate with an official who worked with Thumairy, one witness told the FBI. After meeting Hazmi and Mihdhar, the source told investigators, Bayoumi met with Thumairy at the King Fahad Mosque. (Thumairy has denied that he helped the hijackers.)

Several days later, as Bayoumi was setting up the hijackers’ bank account in San Diego, telephone records gathered by the FBI show that he called Thumairy – one in a series of calls between the two men. Around the same time, Bayoumi also called a Yemeni American imam in San Diego, Anwar al-Awlaki, who would later emerge as a leader of al-Qaeda in the Arabian Peninsula.

Although it was known that Awlaki had contact with the hijackers in San Diego, he was still viewed as a Muslim moderate for several years after the 9/11 attacks. But newer FBI documents suggest that Awlaki might have played a more significant role in working with Bayoumi to help Hazmi and Mihdhar.

Awlaki was killed in Yemen in 2011 by a drone strike ordered by President Barack Obama.

Several of the more recently declassified FBI documents, including the 2021 synthesis , also shed new light on the relationships of Bayoumi and Thumairy with key figures in the Saudi religious network that operated in the United States.

Between January and May 2000, the report notes, two cellphones “associated with Bayoumi” registered 24 calls to the Saudi Consulate, 32 to the embassy in Washington and 37 to the Saudi cultural mission in Virginia.

Bayoumi made a series of calls right before and after the hijackers arrived in San Diego to Mutaib al-Sudairy, a Saudi cleric who had visited him in California months earlier. Sudairy, who nominally worked as an administrative officer at the Saudi Embassy in Washington, lived for several months in Missouri with a Palestinian American man who reportedly procured satellite phones and other equipment for Osama bin Laden. Sudairy was also linked “to suspected Al Qaeda operatives in Saudi Arabia,” the report says.

Both Bayoumi and Thumairy were also repeatedly in touch with Musaed Ahmed al-Jarrah, a key figure in the Saudi religious network who was a senior figure in the Islamic affairs section of the Washington embassy, FBI documents indicate.

Jarrah “had a controlling, guiding and directing influence on all aspects of Sunni extremist activity in Southern California” and “numerous contacts with terrorism subjects throughout the US,” the 2021 report states.

At the Washington embassy, Jarrah also acted as a senior officer of the Saudi intelligence service. He was a close aide to the longtime ambassador, Bandar, and worked for him again after Bandar returned to the kingdom to lead the National Security Council; Jarrah was forced by the FBI to leave the United States because of his suspected extremist ties.

Neither a spokesperson for the Saudi Embassy nor lawyers for the Saudi government responded to questions about the FBI documents’ assertions about the roles of Bayoumi, Sudairy, Jarrah and Bandar.

While the Bayoumi revelations and others might be embarrassing for the Saudi government, it remains unclear why successive US administrations kept so much of the 9/11 investigation secret for so long. As recently as 2020, former attorney general William Barr blocked the disclosure of FBI and CIA documents on the grounds that they constituted state secrets.

Some of those documents were later released under an order that President Joe Biden signed in September 2021, days before the 20th anniversary of the attacks. But some records being sought by the 9/11 plaintiffs are still being withheld, including call logs from a cellphone that Bayoumi is believed to have lent to visiting Saudi operatives.

In response to questions about the 2021 report and the Bayoumi disclosures, the FBI said in an email that it had “nothing to add about the documents released through the Executive Order process.”

Among the many unanswered questions about Bayoumi, Thumairy and others who aided the hijackers, the biggest is who might have organized that effort.

Although the Saudi intelligence services and the kingdom’s religious network sometimes worked in concert, they had distinct agendas. The religious network sometimes acted independently or even at cross-purposes with the government.

Given the abiding mystery over how the CIA lost track of Hazmi and Mihdhar in Malaysia, some former FBI investigators have speculated that Bayoumi might have been asked to approach the hijackers as part of a US or Saudi intelligence operation to recruit them. At the time, former officials have said, the CIA was trying desperately to develop sources inside al-Qaeda.

The CIA has long denied that it allowed the hijackers to come into the United States as part of a failed recruitment effort. That theory gained some currency with statements by a former White House counterterrorism coordinator, Richard Clarke, that it was a plausible explanation for the CIA’s failure to track the first two hijackers and its long refusal to alert the FBI to their presence in the United States.

But such a theory does not explain the CIA’s apparent lack of attention to Hazmi and Mihdhar’s whereabouts or Bayoumi’s sometimes disinterested relationship with them.

Whether the answers to such questions might emerge from the federal lawsuit remains to be seen.

Netburn, the magistrate, had notified the plaintiffs that she would only reopen discovery in the case if there were “extraordinary circumstances.” So far, she has not been persuaded that the new information about Bayoumi’s work for the Saudi intelligence agency meets that standard.

The Saudi government, which has long denied that Bayoumi or Thumairy aided the hijackers on behalf of the kingdom, dismissed the plaintiffs’ appeals to reopen discovery as “more of the same.” Starting in the fall, the court will also hear arguments on a motion by the Saudi government to dismiss the case.

“It’s clear from this evidence that Saudi intelligence was at the center of the network that aided the hijackers as they prepared for the attacks that killed my father,” said Peter Brady, the son of a finance executive, Michael G. Jacobs, who died in the World Trade Center. “We urge the courts to allow further inquiry. Our families — and the American public — deserve answers and accountability.”

Tim Golden is an editor at large at ProPublica, concentrating on national security, foreign policy and criminal justice. Follow him on Twitter @Tim_Golden. Sign up for The Big Story newsletter to receive Pro-Publica stories like this one in your inbox.

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