Amid signs the spy case against him is fizzling, Yee is released from confinement, only to face new charges of adultery and downloading pornography.

Olympia, Wash.
October 2003

At the doorway of her small apartment in Olympia, Huda Suboh was confronted by two federal agents. They had something to tell her about her husband, Capt. James Yee.

Your husband is having an affair, they said. A female Navy officer at Guantánamo.

For Suboh, the allegation, whether she believed it or not, could not have hurt more. The case already had caused so much pain: the questions from investigators, the searches of her home, reporters knocking on her door.

And now this.

As she broke down in tears, the agents pulled out photographs, one after another, of suspected terrorists. Did her husband associate with them, they asked.

One she recognized, Airman Ahmad Al Halabi. But to the others, the men with the long beards, Suboh sobbed, shaking her head "No."

Yee's affair had been discovered after his arrest. For the investigators, the chaplain's infidelity meant more than a violation of military code. It deepened their suspicions. Spies typically led double, even triple lives. This fit the pattern.

"It rocked our world," recalled Capt. Theo Polet, the counterintelligence agent who had launched the investigation.

For Suboh, the news of her husband's affair would remain a painful secret — for now.

In just a few days, she would get to see her husband. It had been six weeks since his arrest, and the military finally had agreed to a family visit.

She and the couple's 3-year-old daughter, Sarah, flew to the East Coast and with Yee's parents and his younger brother, Jason, drove to the Naval Consolidated Brig in Charleston, S.C.

Since the 9/11 terrorist attacks, the brig had gained notoriety for the terrorism suspects held within its beige walls. There was Jose Padilla, accused of trying to import a so-called dirty bomb; Yaser Hamdi, a U.S.-born Saudi who allegedly fought alongside the Taliban; and now there was Suboh's husband, a Muslim chaplain who had built a career on defending Islam within the military.

The austere visitor's room was empty except for bolted-down tables and two guards. Yee was there waiting when Suboh and the family entered. Sarah burst across the room, leaping into her father's arms. He wore green camouflage fatigues, no belt, no boot laces.

Suboh sat down quietly next to him, her face framed by a Muslim scarf.

As his daughter played in his lap, Yee's mother, Fong, could see bruises on his left wrist. Handcuffs, she thought.

As always, Yee was calm, stoic.

"He just said, 'Ma, it's OK,' " Fong Yee recalled. "I guess he didn't want me to make a big deal about it. You know how kids are."

Since his arrival, Yee had been held in solitary confinement in an 8-by-10 cell, not much bigger than those back at Guantánamo. There was a bed and a shelf, both bolted down; a sink and a toilet. The steel door had a slit for a window so guards could peer inside.

For one hour a day Yee was allowed out for exercise. But anytime he moved beyond his cell he was required to wear hand and leg irons, even to talk to his lawyers.

His civilian lawyer, Eugene Fidell, complained that Yee was not being treated as an officer and that he had been denied a prayer rug and a liturgical calendar. Guards refused to tell him the time of day, or the direction of Mecca by which to pray.

On this day, though, there were no handcuffs or leg shackles.

The very fact that the family had been allowed to visit was good news — another signal, his family thought, that the case against him was weakening.

There were other hints that the case was eroding.

Two weeks earlier, the military had filed the first of its formal charges: two counts of mishandling classified information. The charges carried a maximum jail term of two years each but typically resulted in little more than administrative punishment.

Though the investigation was still open, it was a far cry from the news headlines alleging that Yee was at the center of an espionage ring and had been caught aiding the enemy.

Even the tide of news coverage was shifting, raising questions of whether the government had rushed to judgment on a post-9/11 terrorism case.

But investigators still were convinced that Yee was involved in a conspiracy. The lead prosecutor, Navy Lt. Cmdr. Paul LeBlanc, asked for a 45-day delay to give investigators more time to build their case.

LeBlanc's Oct. 16 letter to Maj. Gen. Geoffrey Miller was a revelation of just how sweeping the investigation had become. It involved the FBI, Justice Department, Customs, Air Force, Navy and the National Security Agency, LeBlanc wrote.

There were multiple suspects "who appear to have engaged in a conspiracy, some of whom are from different military services and at least one of whom is a civilian."

It involved "witnesses in different states and countries and tracking international telephone, banking and e-mail transactions."

Miller granted the delay, the first of several he would authorize. And a new, crack prosecution team was brought in headed by Lt. Col. Michael Mulligan.

In Washington, D.C., meanwhile, Fidell was fielding phone calls from reporters, trying to shift public opinion about the case. A Harvard Law graduate, Fidell had served as a military lawyer in the Coast Guard and was president of the National Institute of Military Justice, a nonprofit group of attorneys who specialize in military law.

His top priority was to get Yee out of jail. Frustrated by the military's refusal to free his client, Fidell turned to a higher authority. On Nov. 24, he faxed a four-page letter to President Bush and sent copies to the nation's media.

There's no evidence that the letter ever reached Bush. It didn't matter: Prosecutors already had decided to release Yee. They realized this was no longer a spy case.

Prosecutors still hoped to get Yee for aiding the enemy, a charge that rested on the theory that he was using the prison library to run a secret communication network for detainees. Even now hundreds of books rounded up from Guantánamo cells were being analyzed for evidence of subversion on Yee's part. But that analysis could take months.

All prosecutors had now were the minor charges of mishandling classified information, and a couple more they were about to add. They hoped that Yee, once out of prison, might slip up and contact someone, or say something, that would incriminate him.

On Nov. 25, one day after Fidell's White House letter was sent, Yee was unceremoniously released and reassigned to the chaplain's office at Fort Benning, Ga., while he awaited trial.

But before anybody could celebrate, the military's Southern Command, in a public statement, quickly announced three new charges: downloading pornography from the Internet; making a false official statement; and adultery. Now the world knew the secret Huda Suboh had learned a month earlier.

"It was like them saying, 'We really can't pin anything on you but we're going to get you for this,' " Yee's father, Joseph, said later.

Humiliating as the new charges were, though, his release was the strongest indication yet that the case was evaporating.

Nearly 3,000 miles away, another case against one of Yee's friends also was crumbling.

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