Quote of note:

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

Even now, Defense Department officials refuse to explain in detail how the investigations originated and what drove them forward in the face of questions about much of the evidence.

How Dubious Evidence Spurred Relentless Guantánamo Spy Hunt
By TIM GOLDEN

Capt. Theodore C. Polet Sr., an Army counterintelligence officer at the detention camp for terrorism suspects 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.

The F.B.I. had found that a car belonging to the chaplain, Capt. James J. Yee, had been spotted 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.

Although it was unclear what the activist had done or whether Captain Yee even knew him, Captain Polet took the report to the Guantánamo commander, Maj. Gen. Geoffrey D. 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," Captain Polet said, noting that General Miller's ears turned red with anger. "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 grew much bigger than has been publicly disclosed, spinning into a web of counterintelligence investigations that eventually involved more than a dozen suspects, a handful of military and civilian agencies and numerous agents in the United States and overseas.