Capt. Theodore Polet Sr., an Army counterintelligence officer for the terrorist-detention camp at Guantánamo Bay, Cuba, had just begun investigating a report of suspicious...

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Capt. Theodore Polet Sr., an Army counterintelligence officer for the terrorist-detention camp at Guantánamo Bay, Cuba, had just begun investigating a report of suspicious behavior by a Muslim chaplain at the prison last year when he received what he thought was alarming new information.

According to a source at the FBI, he said, a car belonging to the chaplain, Capt. James Yee, had been seen twice outside the home of a Muslim activist in the Seattle area who, years earlier, had been a host for a visit from Omar Abdel Rahman, the militant Egyptian cleric convicted in a 1993 plot to blow up various New York landmarks.

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Before being sent to Guantánamo, Yee had been stationed at Fort Lewis in Pierce County.

Although it was unclear what the activist had done and whether Yee had even met him, Polet took the report to the Guantánamo commander, Maj. Gen. Geoffrey Miller, and laid it out in stark terms.

“I said we had found something that connected Yee with a known terrorist supporter in Washington state, and at that point, he got very upset,” Polet said, noting that Miller’s ears turned red. “This became far more serious than a basic security violation. The case was going to get bigger.”

In fact, documents and interviews show that the case got much bigger than has been publicly revealed, spinning into a web of counterintelligence investigations that eventually involved at least 19 possible suspects, a handful of military and civilian agencies and dozens of agents in the United States and overseas.

Within less than a year, however, the investigations into possible espionage and aiding the enemy at Guantánamo grew into a major source of embarrassment for the Pentagon, as the prosecutions of Yee and another Muslim serviceman at the base, Airman Ahmad Al Halabi, unraveled dramatically.

Even now, Defense Department officials refuse to explain in detail how the various investigations originated and what drove them forward in the face of questions about much of the evidence. The officials have defended their actions, emphasizing that some of the inquiries continue.

But confidential investigative documents, court files and interviews show that the military’s pursuit of Yee and others drew significantly on questionable evidence and disparate pieces of information that, like the car report, linked him tenuously to people suspected of being Muslim militants in the United States and abroad.

Officials familiar with the inquiries said they also fed on petty personal conflicts: antipathy between some Muslim and non-Muslim troops at Guantánamo, rivalries between Christian and Muslim translators, even the complaint of an old boss who saw Al Halabi as a shirker.

The military’s aggressive approach to the investigation was established at the outset by Miller, the hard-charging Guantánamo commander. Along the way, some investigators and prosecutors suggested that the job of ferreting out spies at the base had put them, too, on the front lines of the fight against terrorism.

Perhaps the most aggressive was the lead Air Force investigator in the Al Halabi case, Lance Wega, a probationary agent who took over the case after barely a month on the job. While he was later commended by superiors and rewarded with a $1,986 bonus, testimony showed Wega mishandled important evidence.

Ultimately, Air Force prosecutors could not substantiate the vast majority of the charges they brought against Al Halabi, a translator at Guantánamo, who had faced the death penalty.

He pleaded guilty to four minor charges of mishandling classified documents, taking two forbidden photographs of a guard tower and lying to investigators about the snapshots. He was sentenced to the 10 months imprisonment he had already served.

Yee, a West Point graduate who was held for 76 days in solitary confinement, charged with six criminal counts of mishandling classified information and suspected of leading a ring of subversive Muslim servicemen, was convicted only of noncriminal charges of adultery and downloading Internet pornography. His conviction was dismissed altogether last April.

Another Guantánamo translator, Ahmed Mehalba, has been jailed since September 2003 on charges that he lied to investigators about carrying a computer disc containing classified Guantánamo documents to Egypt.

Coloring much of the episode, interviews and documents indicate, were simmering tensions over the military’s treatment of the roughly 660 foreign men who were then held at Guantánamo without charge.

“Lots of the guards saw us as some sort of sympathizers with the detainees,” Al Halabi recalled in one of several interviews. “We heard it many times: ‘detainee-lovers,’ or ‘sympathizers.’ “

Al Halabi has emphasized his loyalty as a naturalized American citizen. While insisting that he was careful not to share his views with anyone but close friends at Guantánamo, he said he was one of many servicemen and translators there who were deeply uncomfortable with the way detainees were treated.

“I did disagree with what was going on,” he said. “These people had been there forever and were blocked from the legal system. This country stands for justice and human rights, and there we were at Guantánamo doing none of that.”