After seven years of litigation, two trips to a federal appeals court and $3.8 million worth of lawyer time, the public has finally learned why a wheelchair-bound Stanford University scholar was cuffed, detained and denied a flight from San Francisco to Hawaii: FBI human error.

FBI agent Kevin Kelley was investigating Muslims in the San Francisco Bay Area in 2004 when he checked the wrong box on a terrorism form, erroneously placing Rahinah Ibrahim on the no-fly list.

What happened next was the real shame. Instead of admitting to the error, high-ranking President Barack Obama administration officials spent years covering it up. Attorney General Eric Holder, Director of National Intelligence James Clapper, and a litany of other government officials claimed repeatedly that disclosing the reason Ibrahim was detained, or even acknowledging that she'd been placed on a watch list, would cause serious damage to the U.S. national security. Again and again they asserted the so-called "state secrets privilege" to block the 48-year-old woman's lawsuit, which sought only to clear her name.

Rahinah Ibrahim.

Holder went so far as to tell the judge presiding over the case that this assertion of the state secrets privilege was fully in keeping with Obama's much-ballyhooed 2009 executive branch reforms of the privilege, which stated the administration would invoke state secrets sparingly.

"Under this policy, the Department of Justice will defend an assertion of the state secrets privilege in litigation, and seek dismissal of a claim on that basis, only when necessary to protect against the risk of significant harm to national security," reads an April signed declaration from the attorney general to U.S. District Judge William Alsup, who presided over the Ibrahim litigation in San Francisco.

The state secrets privilege was first upheld by the Supreme Court in a McCarthy-era case and generally requires judges to dismiss lawsuits against the United States when the government asserts a trial threatens national security.

In his declaration, Holder assured Judge Alsup that the government would not be claiming national security to conceal "administrative error" or to "prevent embarrassment" – an assertion that is now nearly impossible to square with the facts.

Elizabeth Pipkin, the San Jose attorney who represented Ibrahim in her legal odyssey pro bono, said the Obama administration should be embarrassed.

"The idea that any of this poses any threat to national security is ridiculous," Pipkin said in a telephone interview. "These government state secret privileges are to protect national security. They are not supposed to be used to cover up government errors."

The Justice Department did not respond for comment.

The Justice Department nearly got away with the cover up, which commenced under the President George W. Bush administration.

At one point, Judge Alsup dismissed the case. A federal appeals court reinstated it in 2012, more than a year after Alsup tossed it. A month before Ibrahim's trial, the judge said he learned the Kafkaesque truth. "I feel that I have been had by the government," he said in a November pretrial conference.

Last week he laid it out all in his final order in the case, ruling for Ibrahim following a five-day, non-jury trial that was conducted largely behind closed doors in December.

At long last, the government has conceded that plaintiff poses no threat to air safety or national security and should never have been placed on the no-fly list. She got there by human error within the FBI. This too is conceded. This was no minor human error but an error with palpable impact, leading to the humiliation, cuffing, and incarceration of an innocent and incapacitated air traveler. That it was human error may seem hard to accept — the FBI agent filled out the nomination form in a way exactly opposite from the instructions on the form, a bureaucratic analogy to a surgeon amputating the wrong digit — human error, yes, but of considerable consequence. (.pdf)

Ibrahim was a Stanford University doctoral student in architecture and design from Malaysia and was headed to Hawaii to give a paper on affordable housing. Wheelchair-bound after just having a hysterectomy, she was handcuffed, detained for hours at San Francisco International Airport and denied her pain medication until paramedics arrived in 2005. She was eventually released and allowed to fly to her home country of Malaysia.

She sued, seeking to learn if she was on the no-fly list and to clear her name. Her case ping-ponged across the legal landscape for years as the government tried everything it could to have the lawsuit tossed.

The woman was even barred a return flight for her own trial. So was one of her daughters, a U.S. born American citizen, who witnessed her mother's humiliation at the San Francisco airport.

It's not the first time the government pushed the envelop in declaring state secrets in litigation. The same was true when the state secrets privilege was born in a 1953 Supreme Court case.

At the time, three widows of civilians whose husbands died in a Georgia military aircraft crash sued. The government refused to release the accident report, on the grounds that it would disclose information about secret military equipment. That report was declassified in 2004, however, and did not mention any secret military equipment.

"Praise to God for this win," Ibrahim, who is in Malaysia, said in a statement provided by her lawyers.

Here are selected quotations, gleaned from the public court docket, of government officials who sought to have Ibrahim's case dismissed over a span of two presidential administrations:

Director of National Intelligence James Clapper. Photo: Carolyn Kaster/AP

"My assertion of the state secret and statutory privileges in this case precludes defendant or any other agency from making any response, including through document production or deposition testimony, that would serve to disclose classified information regarding plaintiff or any other individual; the sources, methods, and means by which classified information is collected; and information which would confirm or deny whether information regarding plaintiff or any other individual is in NCTC's TIDE database." – James Clapper, director of national intelligence, April 23, 2013.

"Second, I agree with the FBI that disclosure that an individual is not a subject of an FBI counterterrorism investigation could likewise reasonably be expected to cause significant harm to national security. As the declaration explains, if the fact that some persons are not subject to investigation is disclosed, while the status of others is left unconfirmed, the disclosure would reveal that the FBI has had an investigative interest as to those other particular persons. Allowing such disclosures would enable individuals and terrorist groups alike to manipulate the system to discover whether they or their members are subject to investigation. Further, individuals who desire to commit terrorist acts could be motivated to do so upon discovering that they are not being monitored." – Eric Holder, attorney general, April 23, 2013.

Attorney General Eric Holder. Photo: USDOJ

"But a trial on the central harm identified by Plaintiff and the Court — the alleged inability to travel internationally, including to the United States — cannot fully be adjudicated without the information subject to the state secrets privilege." – *Paul G. Freeborne, Department of Justice senior trial counsel, Nov. 12, 2013.

"Public disclosure of the identity of individuals on the No Fly List or Selectee List would compromise the safety and security of passengers by providing terrorists with information that may reveal which of their members have been compromised, and which of their members may board an aircraft without any form of enhanced security. For these reasons, TSA's regulations expressly prohibit the disclosure of the contents of Security Directives and Emergency Amendment…" – Joseph C. Salvator, Transportation Security Administration then-deputy assistant administrator for intelligence, May 22, 2006.

"Plaintiff directly challenges the No Fly list, arguing that her alleged placement on this list violated her First and Fifth Amendment rights, and caused her to be arrested by local law enforcement personnel allegedly in violation of her Fourth Amendment rights. These claims are inescapably intertwined with the procedures and merits of the No Fly list itself and must, therefore, be dismissed. – John R. Tyler, Department of Justice trial attorney, May 22, 2006.