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On Nov. 13, 2009 when the attorney general announced the planned trial, “Holder stubbornly stayed on message, saying over and over again that their case was strong and he was confident the Justice Department would win convictions,” writes Klaidman. “Then he obliquely alluded to the secret evidence that he believed was his trump card: ‘I will say that I have access to information that has not been publicly released that gives me great confidence that we will be successful in the prosecution of these cases in federal court.’”

From a legal perspective, the recordings were a vast improvement over evidence obtained through harsh interrogation techniques inflicted on Mohammed by CIA interrogators.

Mohammed was water boarded 183 times during his interrogations. In contrast, his conversations with other inmates would be free of the legal taint resulting from a variety of harsh interrogation techniques, which included pouring water over the immobilized prisoner’s face to impose the sensation of drowning.

The alternative was for military prosecutors to use clean-team statements, interviews conducted by FBI interrogators with no involvement in the CIA’s enhanced interrogation program, but some federal judges had thrown out clean-team evidence as well, arguing that once a defendant had been tortured, any future testimony he might give to American authorities would be tainted, Klaidman writes.

James Connell, an attorney for Ali Abd al-Aziz Ali, one of the defendants in the Sept. 11 trial at Guantanamo, said that he was unaware of any recordings, but that if it turns out that they exist he would ask for them to be turned over to the defense to be evaluated. Any statements made by a defendant that are in the possession of the government would be subject to discovery under military commission rules, Connell said.

Cheryl Bormann, an attorney for another of the defendants, Walid bin Attash, said she wouldn’t be surprised if the government had surreptitiously recorded her client’s conversations.

“Their entire scheme here, meaning the U.S. government, has been to collect intelligence,” Bormann said. “The system was designed to do that and prosecution was an afterthought.”

Associated Press writer Ben Fox in San Juan, Puerto Rico, contributed to this report.