By Raymond Bonner, ProPublica

As the Senate debated a proposal this month that would have barred gun sales to people on the government’s terrorism watch lists, Republicans decried the lists as unfair, unreliable and un-American. “There’s no due process or any way to get your name removed from it in a timely fashion,” Sen. Marco Rubio told CNN. “This is not a list you can be certain of,” Jeb Bush said. Mike Huckabee asserted that some people end up on the no-fly list due to “suspicion, not necessarily even so much as probable cause.”

Rahinah Ibrahim, a Malaysian architect with a doctorate from Stanford, knows from personal experience that they have a compelling point. Ibrahim is the only person since the 9/11 attacks to file a court challenge that ultimately removed her name from the watch lists. It took her almost a decade to prevail in court and even that victory has proved pyrrhic for her. While a federal judge agreed that her inclusion on the no-fly list was groundless, she remains unable to obtain a visa that would allow her to visit the United States even to attend academic conferences. A close look at her case by ProPublica provides dramatic evidence of what was argued this month in Washington: It is indeed remarkably easy to get on the list and nearly impossible to get off.

The questions of terrorism lists and visas appear likely to take center stage in the coming months. While the Senate rejected the amendment barring gun sales, Connecticut’s governor imposed just such a ban on a threat that is more theoretical. Between 2004 and 2014, more than 2,000 people on the government’s watch lists purchased firearms in the United States, according to a study by the Government Accountability Office. Questions are also emerging about how Tafsheen Malik, one of the perpetrators in the San Bernardino terrorism attack, managed to get a visa to join her husband despite her pro-jihadi postings on social media.

Taken together, the two cases offer a disturbing look at the ability of U.S. authorities to effectively and fairly guard the border.

***

Ibrahim’s saga began on Jan. 2, 2005. A devout Muslim, she got up before dawn and said her morning prayers. A friend drove her up Highway 101 from San Jose to the San Francisco International Airport. She was booked on United Airlines Flight 41. Ibrahim planned a stopover in Hawaii, where she would deliver a paper at a prestigious conference, before continuing to Malaysia.

The 44-year-old mother of four felt good about her forthcoming trip although she was still in pain from an emergency hysterectomy months earlier. She had just completed four years of demanding course work while also working as a volunteer at the Stanford hospital. She had just passed her oral exams, a considerable accomplishment for someone who had grown up in rural Malaysia and not been out of the country until she was 18.

When Ibrahim, wearing a hijab that allowed not a strand of her brown hair to show, reached the counter, the ticket agent looked at her reservation and summoned a supervisor. Soon, Ibrahim saw two San Francisco police officers striding purposefully through the terminal. After speaking with the supervisor, the officers told Ibrahim that she was under arrest, handcuffed her and marched her through the crowded terminal to a police car that drove her to the airport police station. Inside, as she would later recall, she found herself in a deeply uncomfortable setting, “a handcuffed Muslim woman surrounded by three male policemen.” The officers locked Ibrahim in a cell where she sat on a cold, stainless steel bench and cried, the scar across her abdomen aching.

Ibrahim had no idea why she had been detained. She explained to the police that two FBI agents interviewed her just nine days earlier and she showed them the business card that one of them, Kevin Kelley, had given her. Kelley was a member of the South Bay Joint Terrorism Task Force in San Jose. He had asked about her academic work (her area of concentration at the engineering school was affordable housing); about her husband (he’s very progressive and had allowed her to pursue her career, something most men in her conservative country would not do); and about Jemaah Islamiyah, a terrorist group created in Malaysia but best known for bombings of night clubs in Bali. Ibrahim told Kelley she didn’t know much about Jemaah Islamiyah beyond headlines on the Internet, but that she was a member of Jemaah Islam Malaysia, a professional organization for people who had studied in the United States and Europe and encouraged the practice of more moderate forms of Islam.

After she had been detained at the police station for more than two hours, an official from the Department of Homeland Security, Lee Korman, showed up. He apologized to Ibrahim for her arrest and told her that she had been removed from the no-fly list and was now free to fly. It was the first time Ibrahim knew she was on the no-fly list.

Before the 9/11 attacks, there were perhaps a dozen people worldwide on America’s no-fly list. The numbers soared after the attacks and by 2013 there were some 47,000 individuals on the list, according to a Justice Department audit. Grandmothers, infants, honorably discharged veterans, and the disabled have found themselves barred from boarding. A few notorious cases made headlines, such as when Sen. Edward Kennedy was stopped several times—because, it turned out, there was a “T. Kennedy” on some agency’s terrorist watchlist. Kennedy’s name was, of course, removed. For tens of thousands of others, it was not so easy.

The no-fly list is part of the post 9/11 security apparatus, which is a labyrinth of euphemisms and acronyms. The effort is coordinated by the Terrorism Screening Center (TSC), a multi-agency group of officials managed by the FBI in coordination with the CIA. All federal departments and agencies are responsible “for collecting information about potential terrorists or attacks” and sharing that information with the FBI or the CIA, either of which can “nominate” individuals for inclusion in the Terrorist Screening Database (TSDB).

From that database, names are passed “downstream” (in bureaucratic jargon) to the so-called “frontline” agencies—for example, to the Transportation Security Agency (TSA), which administers the no-fly list, and to the State Department, where the names are put into the Consular Lookout and Support System (CLASS), which American consular officers around the world call up when a foreigner applies for a visa.

State and local law enforcement officials have access to the database, which now has some 700,000 records. A police officer pulling over a driver for speeding can check the name on the driver’s license against the TSDB. In addition, the lists are shared with more than 20 foreign governments.

An FBI agent need only have a “reasonable suspicion” to “nominate” someone, the FBI guidelines say. It is supposed to be more than “a mere guess or hunches.” But, as Huckabee noted, the standard is well short of the probable cause the police need to arrest a person.

***

Ibrahim was born in 1969, the second of five children, into modest circumstances, her father a mid-level civil servant. She inherited school uniforms and textbooks from her older sister, and then passed them on to her younger one. Neither of her parents had finished high school, and they pushed their children to get an education.

Ibrahim had mild dyslexia and was something of a loner in school who found solace in drawing. She finished first in her high school class, and was one of 25 students nationwide selected to study in the U.S. She had been on an airplane only once before, a small one, to return home from boarding school when her father died. When the flight stopped for a layover in Hong Kong, Ibrahim got separated from the rest of the group. Another student in the honor’s program, Mustafa Kamal, the son of primary school teachers in a small rural town, volunteered to find her. Kamal would continue chasing Ibrahim, changing her life—romantically, unconventionally, profoundly. Ibrahim enrolled in the University of Washington to study architecture; Kamal studied civil engineering at California State University, Long Beach. After a long-distance, telephone romance, they married in the summer between their third and fourth years. Ibrahim graduated with honors in 1984 after the birth of the couple’s first child and moved to Southern California to study for a master’s at the Southern California Institute of Technology in Santa Monica.

Kamal assumed primary responsibility for domestic chores. “I was a stay-at-home dad,” he said. He was becoming Americanized. Evenings he watched the ABC News with Peter Jennings, and he was such a diehard Los Angeles Lakers fan that he and his friends would adjust the time of their evening prayers so they could watch the games on television.

“I always feel in love with America,” Kamal told me in an interview in Malaysia. “We consider America our second home.” The years in the United States had a profound impact. “I would say that we grew up in the States. It changed our perspective on the world.” One of his favorite television programs was Meet The Press, which he liked to watch “just to see how these people argue.” On his Facebook page, Kamal lists Henry Kissinger’s Diplomacy as one of his “likes.”

Living in America also changed their approach to Islam. They began to practice their religion in a more Western context. “We call it progressive Islam,” Ibrahim told me, during the only interview she has given about her experiences.

After Ibrahim got her master’s degree, the family returned to Malaysia and she launched her career as an architect. At the age of 32, and pregnant with her fourth child, Ibrahim became the first female lecturer at University Putra Malaysia, a 7,500-acre campus 12 miles south of downtown Kuala Lumpur. She was soon intellectually restless and applied to Stanford, surprised when she was accepted.

In 2000, Ibrahim returned to the U.S. with an F-1 student visa. Kamal remained in Malaysia. He was the managing director of an environmental consultancy business and had become deeply committed to international relief work. Kamal traveled to Palo Alto every three months to visit his wife.

***

On March 10, 2005, 10 weeks after her encounter at the San Francisco airport, Ibrahim was set to fly from Malaysia to Stanford with plans to put the final touches on her doctoral thesis. At Kuala Lumpur’s gleaming, modern airport, when she reached the Cathay Pacific counter, she put her bag on the scale—it was filled with presents for patients at the Stanford hospital where she had worked as a volunteer. A supervisory agent asked her to step out of line, and she watched as he made and received calls on his mobile phone. She was puzzled. Korman had told her she had been taken off the no-fly list; she gave Korman’s card to the supervisor. At 9:25, five minutes before the gate was to close, the agent told Ibrahim that he had spoken with the American embassy. Her visa had been revoked.

She was angry and perplexed. Why would the State Department do such a thing?

And so Ibrahim began the laborious process of trying to clear her name of an accusation about which she knew nothing.

She filled out the form for people who feel they are wrongly on the no-fly list. Called the Travel Redress Inquiry Program report (TRIP), it provides little in the way of relief. People get to lodge their complaints. When foreign nationals like Ibrahim are involved, the government declines to confirm or deny their presence on any lists but sends a form letter that says “applicable records” have been reviewed. The letter assures travelers that corrections to the records have been made if “warranted.”

***

In January 2006, a year after Ibrahim was shackled in San Francisco, she filed a lawsuit in federal district court in San Francisco against a litany of federal agencies. She was not asking for monetary damages, or compensation of any sort. She only wanted her name removed from the no-fly list and any other terrorism databases.

Ibrahim was represented pro bono by a small law firm in San Jose, California, McManis Faulkner. “I wanted this case in a heartbeat,” said James McManis, whose legal hero is Clarence Darrow. “What they did to this woman was just outrageous.”

The odds against Ibrahim were beyond astronomical. No one had ever prevailed in a legal challenge of the watch lists. The case was assigned to Judge William Alsup, a demanding, hard-working jurist who began his trials at 7:30, about two hours before his colleagues on the federal bench.

The government moved to dismiss, arguing that by law, challenges to Transportation Security Administration (TSA) rulings must be filed before the U.S. Court of Appeals, not the district court. Alsup agreed. Case dismissed.

Ibrahim’s lawyers appealed to the Ninth Circuit. The lead lawyer at the time, Marwa Elzankaly, was only three minutes into her argument when Judge Alex Kozinsky interrupted, and he didn’t let up, peppering her with questions. Kozinsky was the court’s chief judge, a gregarious, outspoken libertarian-leaning intellectual. Elzankaly stood at the lectern, pen in her right hand, scribbling notes on a yellow legal pad, answering the questions with impressive poise.

It wasn’t as easy for the Justice Department lawyer. If the court had no jurisdiction, how was the plaintiff to get off the no-fly list?, Kozinsky wanted to know. “If not here, where? If not now, when?” said Kozinsky, whose parents were Holocaust survivors. “It’s from the Talmud, you know.” The government lawyer was unaware of the saying.

The appellate court ruled in Ibrahim’s favor, 2-1. The Terrorist Screening Center actually determined who was on the no-fly list, not the TSA, Kozinsky wrote for the majority.

The case was sent back to Alsup for trial.

The Justice Department again moved to dismiss. Ibrahim could not avail herself of constitutional protections because she was not a citizen, nor did she live in the country, the government argued. Again, Alsup agreed. “She is an alien who voluntarily left the United States and thus voluntarily left her constitutional rights at the water’s edge,” he wrote, and dismissed the case. Again Ibrahim appealed. And again, the government lost, 2-1.

Ibrahim had a “significant voluntary connection” with the United States—her time at Stanford; continuing discussions with professors; plans to return—and that allowed her to raise constitutional issues, the appeals court said.

The judges were troubled by the watch list system. The Terrorist Screening Database had grown by over 700 percent since its inception, and 20,000 records were being added a month, the court noted. The judges found that the implementation of the no-fly list was problematic. “Tens of thousands of travelers have been misidentified because of misspellings and transcription errors in the nomination process, and because of computer algorithms that imperfectly match travelers against the names on the list,” the majority wrote.

Meanwhile, the national security bureaucracy seemed uncertain whether Ibrahim was or was not a terrorist, according to the documents unearthed by her lawsuit.

In December 2005, 11 months after Homeland Security agent Korman told Ibrahim that she had been removed from the no-fly list, Ibrahim was put on the list of terrorist suspects that was sent to Australia (TACTICS), and to Canada (TUSCAN). (She had never visited either country, and had no plans to.)

In September 2006, she was completely removed from the Terrorist Screening Database, with federal officials concluding there was no “nexus to terrorism” involved in her case.

Six months later, in March 2007, Ibrahim reappeared in the database.

Two months after that, she was again removed.

The reasons for all these moves remain unknown to Ibrahim, or her lawyers, and were not further explained in the passage of the trial record that summarized her changing status.

In 2009, Ibrahim applied for a visa so that she could go to San Francisco to work with her lawyers. When she went to the American embassy in Kuala Lumpur to pick it up, a consular officer slid a “Dear Visa Applicant” form letter through a slot in the bulletproof glass. Somehow, she was back on the list again.

“This office regrets to inform you that your visa application is refused because you have been found ineligible under the following section(s) of the Immigration and Nationality Act.” There was a check in the box beside “212(a)(3)B.” There was no explanation of what the section is. Ibrahim asked the consular officer. “(Terrorist),” he wrote on the form.

For the first time, Ibrahim knew that the United States government considered her a terrorist.

Ibrahim’s tribulations with the American government contrasted with her triumphs at the Malaysian university. She became a senior lecturer in November 2006; associate professor six months later; full professor in 2011, when she was named dean of the faculty of architecture and design. Her rapid ascent generated some grumbling, envy, and enmity among her colleagues, virtually all men. She was acquiring an international reputation in the field of affordable housing—the list of academic papers in her c.v. ran to more than 10 pages—and she was invited to conferences around the world. The country she most wanted to visit—the United States—would not admit her. The Academy of Sciences of Malaysia collaborated with the New York Academy of Sciences, but she couldn’t attend meetings when they were in New York. She wanted to explore the establishment of a joint research center with Stanford, which would have been a coup for her university and as well as for the country.

***

Ibrahim’s resolve to clear her name was matched by the government’s determination that she never know anything that might help her, or the public, understand why she was considered a terrorist, why she had been on the no-fly list, why she had been denied a visa. In one legal brief, the Justice Department even redacted the names of 13 law cases, two statutes, one Federal Rule of Civil Procedure, as well as several pages of the argument.

“This is too hard to swallow!” Alsup wrote in one ruling. But swallow it he did and the black ink remained in place. The vast majority of documents in Ibrahim’s case—briefs, motions, letters to the judge, hearing transcripts—contain redactions, from a word or two, to a few paragraphs, to entire pages. This makes it impossible to fully assess the government’s claim that it had reasonable grounds to put Ibrahim on the terrorist list or whether she received due process.

Attorney General Eric Holder Jr. filed an affidavit with the court broadly summarizing the evidence the government was withholding on the grounds that it contained “state secrets,” and public release would harm national security. The government’s claim was sweeping, covering any information that “could tend to confirm or deny” whether Ibrahim “was or was not” the subject of an FBI investigation; “any information (if any) obtained by the FBI from the U.S. Intelligence Community” relating to the reasons for any investigation of Ibrahim “or her associates”; and “information related to whether court-ordered searches or surveillance, confidential human sources, and other investigative or operational sources and methods were used by the FBI.”

Ibrahim’s lawyers were skeptical. Take the matter of whether Ibrahim had been the subject of a terrorism investigation, which Holder had asserted was a “state secret.”

“That’s not a secret. It’s not a secret,” Elizabeth Pipkin, who had taken over as lead lawyer when Elzankaly married and moved back to Egypt, told Alsup during a hearing. And she had the documents to prove it. Kevin Kelley, the FBI agent who interviewed Ibrahim in December 2004, had prepared a report. Ibrahim’s lawyers had obtained it through a request under the Freedom of Information Act.

“You have a document there you want to show me that you got from where, a FOIA request?” Alsup said.

Yes, said Pipkin, who was in her mid-30s but already arguing what older colleagues told her was likely to be the biggest case of her career.

Alsup ruled that Kelley’s interview report was admissible. Pipkin then directed his attention to the number “315” written on the report. The bureau’s File Classification List said “315” was the designation for “International Terrorism Investigations.”

”Where did you get your hands on it?” Alsup asked of the classification list.

“We got it from the FBI’s website,” Pipkin answered.

Alsup, astonished, admitted it into evidence.

***

At 7:30 a.m. on Dec. 2, 2013, one month shy of nine years since her ordeal at San Francisco Airport, Ibrahim finally got her day in court. She wasn’t there, however. She couldn’t get a visa.

In Courtroom 8 on the 19th floor of the federal building in San Francisco’s seedy Tenderloin district, Alsup entered and took his seat, the American flag on his right.

On the first day of the trial, the lawyers and Alsup embarked on a lengthy and contentious discussion about what could be made public, what documents would be sealed, when he would have to close the courtroom. Alsup believed passionately that judicial proceedings should be open. “It’s not so much to protect individual litigants,” he said during one exchange with the lawyers. “It’s to protect the public to have access to what is going on in their public institutions, so that the public will have confidence that decisions are being made in a fair and just and evenhanded way.” Still, at the government’s request, he closed the courtroom at least 10 times during the trial, and ruled in favor of the government in nearly all of its requests to redact or seal the record.

Even when the courtroom was open, only a handful of spectators and one or two journalists were there to witness a bizarre case, one that bolsters assertions that due process is lacking.

The Justice Department’s opening argument—the portion that wasn’t delivered behind closed doors—reads like Alice in Wonderland meets Kafka. “Even if Professor Ibrahim were in the TSDB, a fact that we can neither confirm nor deny on the public record, the government cannot present an explanation for the placement” because it is a state secret, a Justice Department lawyer told Alsup. The government “cannot even respond to Professor Ibrahim’s accusations by confirming or denying whether they are correct,” she added.

The pivotal moments of the five-day trial came when two FBI agents, Debra Lubman and Kevin Kelley, testified. At the government’s request, Alsup closed the courtroom. Every word of Kelley’s testimony is blacked out in the publicly released trial transcript. It is possible, however, to know some of what Lubman and Kelley testified by piecing together un-redacted snippets from other documents in the case, including Alsup’s opinion.

Under questioning from one of Ibrahim’s lawyers, Christine Peek, Kelley testified that five weeks before he had interviewed Ibrahim, he had filled out the FBI’s “Violent Gang and Terrorist Organizations File Gang Member Entry Form.”

Using the boiler-pale language on the form, Kelley said he had opened the investigation on the basis of information from “an informant or individual of unknown reliability” that Ibrahim “frequents a documented group’s area, associates with known group members, and/or affects group dress, hand signals, tattoos, or symbols.”

On the form, there was a vertical row of the watchlists, with a box beside each:

o Lookout and Support System (CLASS);o Interagency Border Information System (IBIS);o TSA No Fly list;o TSA Selectee list;o TUSCAN (shared with Canada);o TACTICS (Australia).

Kelley checked five of the six boxes, leaving blank only “TSA No Fly List.”

How then did Ibrahim’s name end up on the No Fly list?

Kelley testified that he had made a mistake. The form instructed the agent to check the list, or lists, on which he did not want to put the individual. He should have checked the TSA No Fly list and left everything else blank.

On the final day of the trial, during closing arguments, Alsup engaged in an absorbing colloquy with the Justice Department lawyers. He harkened back to the 1950s when “thousands of visas and passports and other things” had been denied to alleged Communists. Often the information on which the denials were based was false, he noted.

He put it in the post—9/11 context.

“Let’s say instead of a Communist, let’s say that the file says this person has contributed money to Al-Qaeda. Is that a good reason to deny somebody, to put them on the watchlist?”

It would be, answered Justice Department lawyer John K. Theis.

“All right,” Alsup replied. “So let’s say it’s completely false; that they never contributed a nickel to Al-Qaeda. In fact, they hate Al-Qaeda. They raise the American flag in their front yard every day. Let’s say it’s totally false. How is that person supposed to know to even send in an affidavit saying ‘I’m not a member—I hate Al Qaeda?’”

He brought up a notorious case from the McCarthy era. “Do you know the story of Robert Oppenheimer and what they did to him?” he asked.

“I don’t, your Honor,” Theis said.

Alsup explained that Oppenheimer, a brilliant physicist, was the head of the Manhattan Project, which developed the atomic bomb. In the early 1950s, he was stripped of his security clearance based on allegations of links to the Communist Party—his wife and brother were members—and of spying for the Soviet Union.

“It was a low point in America’s history that we would have treated a hero like him in the terrible way we did. The information was bogus,” Alsup said. “They suspected him of being a Communist. He was not.”

In 1964, President Johnson awarded Oppenheimer the Medal of Freedom.

***

Alsup issued his opinion on Jan. 14, 2014.

He found that Ibrahim’s ordeal had been caused by Kelley’s error in filling out the form, an error that had led “to the humiliation, cuffing and incarceration of an innocent and incapacitated air traveler.” It was, he wrote, “a bureaucratic analogy to a surgeon amputating the wrong digit.”

Alsup’s next finding was even more startling.

“Government counsel has conceded at trial that Dr. Ibrahim is not a threat to our national security,” he wrote, describing some of the testimony he had heard while the courtroom was closed. “She does not pose (and had not posed) a threat of committing an act of international or domestic terrorism with respect to an aircraft, a threat to airline passenger or civil aviation security, or a threat of domestic terrorism. This the government admits and this order finds.”

So why then had the government blocked her from entering the U.S.?

Alsup provided a hint to the answer in three sentences, easy to overlook in his 38-page opinion, and carefully crafted so as not to reveal any classified information. Under the Immigration and Nationality Act, there are nine grounds for denying a person a visa. “Some of them go beyond whether the applicant herself poses a national security threat,” Alsup wrote. The judge did not list the nine grounds. But the immigration law is a public document. Eight of the categories apply to the applicant. One does not. The ninth basis for turning down a visa application is if the person “is the spouse” of a foreigner who has engaged in any terrorist-related activity in the preceding five years.

Thus, the basis for Ibrahim’s place on the watch lists would appear to be something the law purportedly abhors—guilt by association, or in this case, by marriage.

Alsup ordered the government to do what it said it could not do. “Given the Kafkaesque on-off-on-list treatment imposed on Dr. Ibrahim, the government is further ordered expressly to tell Dr. Ibrahim that she is no longer on the no-fly list.” Alsup also ordered all federal agencies that subscribe to the TSDB to search their records and remove Ibrahim’s name. Both orders were unprecedented.

Huckabee had said it can take as long as two years for a person to clear their name. It took Ibrahim almost a decade. And she wouldn’t have succeeded without the commitment of McManis Faulkner, which Alsup commended for “standing up to our national government and its large litigation resources,” and for doing so without being paid, “at a time that pro bono representation seems to have taken a second seat to money bono.”

***

A few months after Alsup’s ruling, I flew to Malaysia to interview Ibrahim. We met at the university. She was wearing a green headscarf with a cut-glass brooch and a traditional Malaysian dress—a brightly flowered knee-length blouse over a matching skirt that reached to her feet. Raihan, her oldest daughter and a newly minted lawyer, set up a computer on the table and plugged it in. Soon, Pipkin was with us, in voice and picture, via Skype. During the two-hour interview, she did not instruct Ibrahim not to answer any questions, or advise her on what to say. (Pipkin was not present during several subsequent interviews with Ibrahim).

Ibrahim had not read Alsup’s opinion, and I told her that her husband might be the cause of her problems. She looked puzzled. “Is that true, Liz?” she asked.

Pipkin explained what Alsup had said. “Putting two and two together,” it would seem to point to your husband, she told Ibrahim.

It appears that Kamal—and by association, Ibrahim—became snared in the U.S. government’s war on terror as the result of his humanitarian activities. His first humanitarian work, including for victims of the tsunami in Indonesia, was with Jemaah Islam Malaysia, the professional organization. Later, he and Ibrahim established their own humanitarian organization, Action Caring Team Malaysia.

Kamal’s altruism is deeply rooted. ”I like to help people because I saw my father helping poor people,” Kamal told me. His father was a primary school teacher in a small, rural village. ”Old shoes, old socks, even old toothbrushes, he gave them to the students.” Kamal has the same impulses. “If I see somebody who is hungry while I am eating, I’ll say ‘Come have a seat.’”

While his wife was at Stanford, Kamal undertook several humanitarian missions to Mindanao, the predominately Muslim province in the Philippines. A civil war had been simmering there for nearly two decades, waged by Muslims seeking independence from, or at least greater autonomy in, the overwhelmingly Catholic country. The war had created more than 200,000 refugees. When Kamal visited for five days in 2003, providing food for widows and orphans, building wells and schools, restoring mosques, the province had become a front in the Bush administration’s war on terrorism; CIA and FBI agents were all over the place. In addition to the various Muslim liberation groups, Washington covertly sought to obtain information about Abu Sayaff, an organization that had received financial support from al Qaeda in the mid-’90s, but had degenerated into a criminal gang that kidnapped for profit, including several Americans. Above all, Washington was watching Jemaah Islamiyah, the terrorist organization, which was using Mindanao as a training ground.

Former FBI and CIA agents who were working in that area at the time told me that Kamal, by his mere presence in Mindanao doing humanitarian work, would have come to the attention of American intelligence.

There may be another reason Ibrahim ended up on the no-fly list. “Maybe they got the wrong wife,” said an American official who has followed the case closely.

As allowed in Islam, Kamal has two additional wives. It is not something Ibrahim or her husband try to hide. He lists his wives, and posts photos of the families, on Facebook. Altogether, Kamal has 13 children. They often gather at Ibrahim’s house on holidays. “We are one big family,” she told me.

Kamal’s third wife, Kurais Abdullah Karim, a Filipina, could also be a cause of Ibrahim’s problems. A lecturer at the International University of Malaysia, Karim, is from Mindanao and is, as Kamal put it, a “humanitarian activist.” In addition to having her own blog, about fashion, and posting regularly on Instagram, she is an unabashed supporter of the Muslim liberation movement in Mindanao. “The Sweetness of Sacrificing for the Sake of Allah: The Life of a Mindanao Freedom Fighter,” was the title of an article she wrote for Milinea Muslim Magazine. (In 2014, the Philippine government and the secessionist Muslims signed a peace treaty ending more than four decades of civil war.)

Kamal said he has never had any involvement with Jemaah Islamiyah, or any other terrorist organization. Malaysian intelligence and security agencies keep close tabs on Malaysians who go to Mindanao, American and European intelligence officials told me, but they do not have a file on Kamal or Ibrahim. If they did, she would not be allowed to be a professor, let alone dean, at the government university, current and former Malaysian officials said, a conclusion shared by American officials who have worked in Malaysia.

Three months after Alsup issued his opinion, in April 2014, the State Department again denied Ibrahim’s application for a visa to travel to the United States. Explaining that action, the department checked Subsection IX of the Immigration and Nationality Act, the spousal connection category, and also the subsection that says visas shall be denied to anyone who “has engaged in a terrorist activity.” This directly contradicted the testimony of the FBI that Ibrahim is not, and has never been, a terrorist threat.

Earlier this year, Ibrahim applied for a visa under a provision in the immigration law that allows the State Department to grant a waiver to individuals who are otherwise ineligible. She wanted to attend a planning meeting for a joint Stanford-University Putra research center, her longtime dream. The State Department delayed and by the time it granted a one-time waiver, it was too late for Ibrahim to attend. The State Department still considers her ineligible under the terrorism category, and she will have to apply again for a waiver should she seek to come to the United States.