SAN FRANCISCO – In 2005, Rahinah Ibrahim, a visiting scholar at Stanford University, was handcuffed, detained and interrogated for two hours at San Francisco International Airport, after being told she was on a U.S. government watchlist.

Today, eight years later, the 48-year-old Malaysian academic and mother of four became the first person to take the U.S. to trial after being included in America's database of suspected terrorists. At issue: whether someone wrongly watchlisted has a right to formally clear their name in court – and whether the government even has to admit that it placed someone on the list to begin with.

The first-of-its-kind trial could have serious implications for the government's vast secret watchlist system, which contains 875,000 names, according to the most recent figures released this year by the U.S. National Counter-Terrorism Center.

Ibrahim's attorney, Elisabeth Pipkin, told the court that the trial’s purpose was to clear her client’s name. "We want her completely out of the system," she said.

One hurdle in the trial, which is expected to last two weeks, is that the government so far is refusing to defend itself. "The government cannot respond to any of Professor Ibrahim’s claims," said Deputy U.S. Attorney Lily Farel.

The Obama administration maintains that the basic question of whether Ibrahim is on a watchlist or not is a "state secret," and is hence privileged and confidential, even in a civil lawsuit against the government. The federal judge presiding over the lawsuit has sided with federal prosecutors so far.

But as the trial opened today, U.S. District Judge William Alsup was mulling whether to reveal whether the woman is on a list. The judge briefly closed the courtroom to the nearly dozen onlookers in the wooden gallery as government lawyers and the woman’s counsel haggled over the issue behind closed doors.

"I don’t know the answer for sure on this one," Alsup later said in open court.

Ibrahim was a visiting doctoral student in architecture and design when she was detained, handcuffed and questioned for two hours at San Francisco International Airport. Wearing traditional Muslim clothes, including a head covering, she was headed to Kona, Hawaii, to present a paper about affordable housing.

The month before, the FBI 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 earlier video-taped disposition played in open court today.

She told the two FBI agents that she knew of the group "from reading newspapers online." She asked the agents why they were visiting her. "He told me possibly, because you are from Malaysia," according to the deposition.

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

Her deposition testimony is expected to resume early Tuesday in open court.

Her attorney told the judge, who is presiding over the trial without a jury, that the authorities have singled her out because of "inadequate training," "biased training" and "low standards."

"Once you’re in the system, it’s almost impossible to get out," Pipkin said.

Judge Alsup originally tossed the case, ruling that it was about "an alien who voluntarily left the United States and thus left her constitutional rights at the water’s edge." The 9th U.S. Circuit Court of Appeals revived the lawsuit a year ago.

"At this point in the litigation, no court has attempted to determine the merits of Ibrahim’s claims under the First and Fifth Amendments. The parties have not briefed whether her placement on a terrorist watchlist violates her rights to freedom of association, equal protection, and due process," the appeals court wrote.

The evidence and procedures used to place individuals on the list are secret. Also secret are the reviews of people who ask to be removed from that list and from the much larger "selectee list" which allows people to fly, but requires they go through a pat-down or other extra screening.

Following 9/11, the appeals court noted, "tens of thousands of of travelers have been misidentified because of misspellings and transcription errors" and because of "computer algorithms that imperfectly match travelers against the names" on watchlists.

The woman has settled her wrongful detention suit against the San Francisco Police Department and a TSA contractor, which paid her a combined $225,000.

In March of 2005, she submitted a request through the Transportation Security Administration’s "Passenger Identity Verification" program to clear her name.

The TSA responded a year later in a form letter, saying "it has been determined that a correction to records is warranted, these records have been modified." The letter did not state whether Ibrahim was, or was not, on a watchlist.

The woman eventually graduated from Stanford.