A side-by-side comparison of the Pentagon's secret Guantanamo detainee assessment briefs and federal court rulings involving those detainees shows that intelligence analysts and federal judges can reach starkly opposing conclusions, even while relying on the same raw intelligence.

The Pentagon's threat profiles suggest little doubt about the prisoners' alleged terrorism record, but in some cases, federal judges have been unimpressed by those conclusions. The classified Guantanamo assessment reports were obtained recently by The New York Times and shared with NPR.

One such example involves Fouad al-Rabia, a Kuwaiti arrested in the Tora Bora area of Afghanistan in December 2001.

"Detainee is an al-Qaida member who met with Osama bin Laden at least four times and gave him a $1 million U.S. contribution," is the opening statement in the report on al-Rabia. "Detainee provided support to the Taliban and al-Qaida on the Bagram frontline before going to fight at Tora Bora, where he was placed in charge of logistics."

The report went on to allege that al-Rabia may have directed an al-Qaida training camp and provided instruction to some of the al-Qaida members involved in the Sept. 11, 2001, terrorist attacks. Nowhere in the report is there any suggestion that the information on al-Rabia may be unreliable.

When al-Rabia filed a petition for habeas corpus, the federal judge hearing his case, Colleen Kollar-Kotelly, had an opportunity to review all the files on which his threat assessment was based. She was not impressed.

"The Government has failed to provide the Court with sufficiently credible and reliable evidence to meet its burden of persuasion," Kollar-Kotelly wrote. "If there exists a basis for al-Rabia's indefinite detention, it most certainly has not been presented to this Court." She ordered al-Rabia released, and in December 2009, he returned to Kuwait, a free man after eight years at Guantanamo.

Since 2008, the detainees at Guantanamo have been able to challenge their detention through the habeas process, and the court rulings in their cases have made clear that the evidence against them has sometimes been flawed. Only with the disclosure of the previously secret detainee assessments, however, has it become clear how far the government went in making unproven claims about the detainees' alleged terrorist activity.

In the case of al-Rabia, the Guantanamo investigators depended on statements made about him by other detainees, the most important of whom was later judged to be unreliable. Al-Rabia was also subjected to coercive interrogations, where he was confronted with the accusations made against him.

"They initiated a very harsh program," says defense attorney Matthew MacLean, "utilizing a number of techniques that ultimately over a period of several months broke him down to the point that he basically started parroting back to them whatever they said."

MacLean and al-Rabia's other attorneys showed Kollar-Kotelly that the detainee made his "confessions" after first denying the accusations against him, and that he changed course so quickly and thoroughly as to make his confession suspect.

"Al-Rabia's full confession sought to weave together all of the 'evidence' interrogators told al-Rabia that they possessed," she wrote, "even though the 'evidence' is absent from the record in this case."

In fact, Kollar-Kotelly's observation is supported by a line from al-Rabia's assessment brief. "Detainee admits to details only when confronted with the fact that interrogators already know the details," the assessment notes, as if that observation supported al-Rabia's guilt rather than his willingness to provide his interrogators the answers they were seeking. Kollar-Kotelly noted in her opinion that al-Rabia had been told that he could go back to Kuwait if he confessed, but that if he denied the accusations against him, he would have to stay at Guantanamo.

Significant discrepancies between the views of the intelligence analysts who wrote the detainee threat assessments and the judges who analyzed them as part of the habeas process are evident in many other detainee cases.

In his detainee assessment brief, Musab al-Mudwani, a Yemeni, is described as "an al-Qaida operative who planned to participate in terrorist operations targeting U.S. forces in Karachi, Pakistan and possibly inside the United States." That claim is based in part on the circumstances of al-Mudwani's capture following a firefight with Pakistani security guards at the site of a suspected al-Qaida residence in Karachi. Al-Mudwani was also said to have confessed to his al-Qaida associations during interrogations at Guantanamo.

The federal judge who considered al-Mudwani's habeas petition, Thomas F. Hogan, was not persuaded by the government's evidence presentation. Of 26 statements introduced by the government in support of its argument that al-Mudwani should be indefinitely detained at Guantanamo, Hogan threw out 23.

"There is no evidence that he fired a weapon in battle or was on the front lines," Hogan wrote. "There is also no evidence that he planned, participated in, or knew of any terrorist plots. ... The Court fails to see how, based on the record, Petitioner poses any greater threat than the dozens of detainees who recently have been transferred or cleared for transfer."

Hogan also concluded that al-Mudwani, who had been subject to "coercive" interrogation in Afghanistan before being transferred to Guantanamo, had been so traumatized by his interrogation experience that his subsequent testimony was tainted. The judge nonetheless approved the government's request that al-Mudwani remain in detention, pointing out that in his judgment the government had to demonstrate only that al-Mudwani was a "part of" al-Qaida in order to justify his continued detention.

Hogan's willingness to defer to the government on that point may have indicated that he recognized how different the role of an intelligence official may be from that of a federal judge. The first is focused on potential threats to national security and is rigorous about containing them. The second is focused on justice and is rigorous about promoting it.

"They're asking different questions," says Benjamin Wittes, a senior fellow and national security blogger at the Brookings Institution. "Sometimes one will be shown to have been asking the right question, and sometimes the other will be shown to asking the right question. That's why we have different branches of government taking on different responsibilities. It's why we generally don't put intelligence analysts in charge of the law and why we generally don't put judges in charge of intelligence analysis."

An intelligence analyst has to worry about getting as much information from a detainee as possible and may therefore have a reason to keep that detainee locked up. At Guantanamo, there was also an enormous volume of material. The analysts had hundreds of detainees to review. Matthew MacLean, who helped defend al-Rabia, notes that those who decided which detainees were dangerous may not have had the time to assess thoroughly the information on which they based their decisions.

"You can't do it without looking to see what's behind it," MacLean says. "We ultimately were able to do that ourselves with the information the government provided, and the judge was able to see it, too. What any other analyst has been able to see, I couldn't say."

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