Media and congressional attention ramps up the pressure on investigators, who already are scrambling against the clock to find solid evidence to bolster charges against Yee.

JACKSONVILLE NAVAL AIR STATION, Fla.
September 2003

As James Yee sat in a Navy brig, 48 hours after his arrest, Guantánamo's senior commander issued a chilling memo, warning that Yee might be a spy and a flight risk.

Among the charges Yee could soon face, the memo stated, were mutiny, aiding the enemy and other "serious crimes, including espionage, which potentially carries the death penalty."

The Sept. 12 letter, signed by Maj. Gen. Geoffrey Miller, urged military authorities to keep the Muslim chaplain locked up until trial. The case against Yee was moving smoothly and "no usual delays are expected."

Behind the scenes, however, counterintelligence agents had nowhere near the evidence to support the allegations, despite four months of investigation.

In fact, Yee's arrest had caused confusion among investigating agencies, spoiling surveillance plans at a point when agents were working on little more than theories.

James Yee was placed in solitary confinement and barred from contacting his family.

"It wasn't part of anybody's plan to have Yee arrested," said Capt. Theo Polet, the Army counterintelligence agent who had launched the probe. "We were still investigating. But there was never enough evidence to come out with charges of espionage and spying."

Nonetheless, the arrest and the gravity of the potential charges laid out by Miller spurred a new sense of urgency within the investigation. And now the clock was ticking. Prosecutors had 120 days to formally charge Yee and try him by court-martial, according to military law.

On the day Miller's memo was issued, Polet arrived in Jacksonville to view for the first time the documents agents took from Yee the day of his arrest. They included notes that listed detainees, their cell locations and their interrogators.

One agent who viewed the material the day of the arrest thought it was typical paperwork Yee needed for his job. Polet, though, thought it was more ominous, even if it wasn't enough to prove espionage.

"Such information," Polet said in a sworn statement, could enhance the enemy's ability to tailor an attack on the prison camp and "mass fire on a specific location" to free detainees and harm U.S. personnel.

A few days later, Yee and his military lawyer stood before Cmdr. D.J. Gruber, a Navy magistrate at Jacksonville. Relying heavily on Miller's memo and Polet's statement, Gruber ordered that Yee remain in jail until trial.

Yee was driven under guard to Charleston, S.C., and placed in the U.S. Naval Consolidated Brig. He sat in solitary confinement, barred from contacting his wife or family, who had no idea of his whereabouts or his arrest.

The secrecy was soon broken.

Ten days after the arrest, The Washington Times, citing an anonymous source, ran a front-page story detailing the charges in Miller's memo.

The allegations reverberated in a nation already nervously wondering where the next terrorist attacks might come from. Guantánamo, which housed hundreds of suspected terrorists, was too close to home.

The fact that Yee was a graduate of West Point, which had never had a traitor, and that he already was known by the media for his work on behalf of Muslims in the military in the days after 9/11, added to the sensation surrounding the allegations.

The next day, The New York Times, The Washington Post and news outlets across the country led with their own stories.

Already racing against the clock, investigators now faced new pressure.

"Washington went insane," Polet recalled. "The initial knee-jerk reaction ... was 'we've got a terrorist cell operating down at Gitmo [Guantánamo].' I spent many a day on the phone talking to people in Washington, saying 'no, we don't. It's entirely too early to suggest that.' "

Translator Ahmed Mehalba was arrested.

The frenzy grew when Ahmed Mehalba, a civilian translator working at Guantánamo, was arrested Sept. 29 by Customs agents at Boston's Logan Airport.

Mehalba had been returning from a family visit to Cairo, Egypt, when agents, alert to the recent news of Yee's arrest, noticed his Guantánamo badge and conducted a search. They found a disk and documents relating to Guantánamo.

Twelve days later, Col. Jack Farr, an Army reserve colonel in charge of prisoner interrogations at Camp Delta, was arrested at the end of his six-month tour at Guantánamo after classified work documents were found in his luggage as he prepared to board a plane home.

The July arrest of Ahmad Al Halabi, the first person from Guantánamo to be jailed, also was made public for the first time.

Senior military officials and members of Congress voiced alarm over the possibility of security breaches and espionage at the terrorist prison camp.

Gen. Richard Myers, chairman of the Joint Chiefs of Staff, ordered a thorough review of Guantánamo security operations.

On Capitol Hill, Arizona Republican Jon Kyl, chairman of the Senate subcommittee on terrorism, announced he would hold hearings into whether Muslim extremists had "infiltrated" the military.

Another senator, Charles Schumer, D-N.Y., urged the Pentagon to investigate the agencies that endorsed Muslim chaplains for the military. Yee's parents, who had learned about their son's arrest from television and still hadn't spoken to him, suddenly found news trucks lined up outside their Springfield, N.J., home.

Up to that point, the Army had been a point of pride for the family. Not only had Yee gone to West Point, but a younger brother had followed him and was a captain serving in the Middle East. Another brother was an Army surgeon at Fort Lewis, south of Tacoma.

Shaken, his parents initially refused to talk. Gradually they began granting interviews, insisting their son was innocent. Chinese-American and Muslim groups, too, began speaking out on Yee's behalf, suggesting he might have been a target of ethnic and religious profiling.

As Yee remained in solitary confinement, agents with the FBI, the Justice Department, National Security Agency, Army, Navy and Air Force scrambled to build a case. They pored through his computer files, searched his residences at Guantánamo and Olympia, and questioned his wife, family and Muslim linguists at Camp Delta. The linguists' interviews sometimes turned intimidating. Interrogations lasted six to nine hours, some culminating with investigators reading the translators the military's version of their Miranda rights.

Several linguists sought the advice of Lt. Cmdr. Loretta Nygard, a Navy lawyer stationed at the base at the time. "Many believed they had been coerced into waiving their rights," she said in an affidavit. Many also were concerned with polygraph tests they were ordered to take, she said.

Guantánamo investigators, meanwhile, increasingly were focusing on Yee's work in the prison library. Their theory was that Yee and Muslim colleagues, including Al Halabi, were using the library to run a secret communication network for detainees and to pass along subversive literature to help them resist interrogations.

In an operation dubbed "Clean Sweep," security officers boxed up hundreds of books from the library and prisoner cells and sent them to a national intelligence lab in Virginia to be analyzed, searching for clandestine messages that might link Yee to a crime.

Now they had to wait for the results.

Ray Rivera: 206-464-2926 or rayrivera@seattletimes.com