SAN FRANCISCO — Is former Stanford University scholar Rahinah Ibrahim connected to Malaysian jihadists, as the FBI once suggested, or is she the victim of misguided U.S. bureaucrats who erroneously placed her on a U.S. terror watchlist? Is she even on a watchlist at all?

Those are the lingering unanswered questions in the first-of-its kind federal trial challenging a traveler's alleged placement on America's notorious no-fly list. The 48-year-old Malaysian woman’s case against the U.S. government – in which she seeks solely to clear her name – is awaiting a judge’s verdict after a week of testimony, the bulk of it classified and given behind closed doors here in a San Francisco federal courtroom.

But underscoring the Kafkaesque flavor of the trial, there's a real possibility the verdict itself will be kept a secret, even from Ibrahim.

"It is conceivable? If the government continues to keep this information secret from her and the public, and the judge sustains that objection, it is possible we can have a ruling in this case and she would not know the result," Elizabeth Marie Pipkin, Ibrahim’s pro-bono attorney, said in a telephone interview.

Rahinah Ibrahim: Photo: University Putra Malaysia

It’s one of those strange moments in the U.S. legal system, when national security secrecy is allowed to trump transparency.

Ibrahim's saga began in 2005 when she was a visiting doctoral student in architecture and design. On her way to Kona, Hawaii to present a paper on affordable housing, Ibrahim was told she was on a watchlist, detained, handcuffed and questioned for two hours at San Francisco International Airport. She was wearing traditional Muslim clothes, including a head covering.

The month before, the FBI had visited the woman at her Stanford apartment, inquiring whether she had any connections to the Malaysian terror group, Jemaah Islamiyah, according to the woman’s videotaped disposition played in open court.

Now, nearly nine years after the detainment, the San Francisco judge presiding over the non-jury trial is expected to issue a verdict within weeks. But in a case that has been shrouded in extraordinary secrecy – with closed court hearings and non-public classified exhibits – it's possible that the verdict itself will remain a mystery.

The obvious absurdity here rivals a different trial — which was also in a San Francisco federal courtroom — of two American attorneys who sued the U.S. government for intercepting their phone calls without warrants.

In 2006, federal officials accidentally sent those attorneys for the al-Haramain Islamic Foundation documents about the eavesdropping. The documents were removed from the case based on the government declaring them a state secret. Yet the case proceeded anyway, against the government’s objections, with both the lawyers and the government pretending they did not exist and being barred from citing them.

A federal judge eventually awarded the aggrieved lawyers $20,000 each in damages and their lawyers $2.5 million in legal fees after a tortured legal battle where they proved they were spied on without warrants, even as the pertinent documents were excluded as evidence.

That legal fight, however, was all for nothing.

The 9th U.S. Circuit Court of Appeals overturned the verdict last year, ruling Congress did not allow for aggrieved Americans to sue over the government breaching its own wiretapping laws.

Ibrahim, meanwhile, isn’t seeking any monetary damages. She wants to be removed from a U.S. no-fly watch list — that is if she’s on one, and told why she was placed on one if indeed she was blacklisted.

"We want her completely out of the system," Pipkin said in her opening remarks two weeks ago. She emphatically maintains her client has no terror ties.

But even if she's in the watchlist system, that’s "Sensitive Security Information," which forbids disclosing that to Ibrahim, the government maintains. In court papers, the government asserted that U.S. District Judge William Alsup is powerless to publicly state whether Ibrahim is, or is not, one of 875,000 names lodged in one of the government’s vast, secret watchlist database.

"Only certain government agencies, including TSA, may determine whether information is SSI. TSA’s determination is reviewable by the judiciary, but Congress has expressly specified that the review must occur in a court of appeals," wrote Paul G. Freeborne, a Justice Department senior trial counsel in court documents.

Freeborne added that, even if the woman is on the list, and Alsup believes Ibrahim was put on it wrongly, the judge’s hands are still tied in overruling the SSI determination.

"District courts," Freeborne wrote, "simply cannot review TSA’s determination that certain information is SSI, (.pdf) even if they disagree with TSA’s determination; believe that TSA has insufficiently explained the rationale for its determination; or do not believe that TSA properly interpreted its regulations in making its determination."

The woman, who is now a Malaysian professor, was later cleared to leave the United States but has been denied a return visit, even to her own civil trial. Her travel visa was denied.

"We have evidence with her status with respect to the federal watchlist is causing her visa problem," Pipkin said.

The government on Friday, Pipkin said, was to have lodged under seal documents protected by the state secrets privilege demanding that the judge dismiss the case outright.

"It’s quite possible," Pipkin said, "the government could succeed in their state secret assertions without the plaintiff or public ever knowing what happened here."

The woman’s daughter, who is an American citizen and who was with her mother when she was detained at the San Francisco airport nearly nine years ago, was barred by the U.S. government to fly from Malaysia to San Francisco to testify at the mother’s trial.

Judge Alsup had held an evidentiary hearing on the daughter’s matter, some of it in closed court. The outcome has not been made public.

And if any of this couldn’t get stranger, Ibrahim’s attorney actually does know whether her client is on the list. She was given a security clearance by the government so she could represent her client.

But Pipkin, too, is forbidden from disclosing this information to her client.

"It is very strange. No one is more affected than Dr. Ibrahim, yet she is in the dark," Pipkin said. "The lack of transparency is appalling. So much for the right to face your accuser."