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Mohammed’s “learned counsel” is David Nevin, a defense lawyer in Boise, Idaho. Mohammed also is being defended by an Army and a Marine Corps judge advocate.

In addition to deciding on witnesses and whether the charges merit the death penalty, Adm. MacDonald must determine whether he will level the charges against Mohammed contained in a 90-page “charge sheet” brought by military prosecutors.

At some point, the defense will have 60 days to file pretrial motions, which could take months to conclude. Attorneys likely will seek prosecution evidence and ask that Mohammed’s statements be ruled inadmissible at trial.

Mohammed was one of three high-value al Qaeda captives waterboarded by the CIA to obtain information on the group’s structure, financing and planned attacks.

Mr. Stimson said a trial might not start until 2013.

In court appearances in 2008, Mohammed admitted to masterminding the 9/11 attacks and asked the military judge to end motions in the case and let him plead guilty.

The charge sheet states, in part: “In August 1996, [Osama] bin Laden (al Qaeda’s ‘emir’ or leader) issued a public ‘Declaration of Jihad Against the Americans,’ in which he called for the murder of U.S. military personnel serving on the Arabian Peninsula. In 1996, Khalid [Shaikh] Mohammed met with [Osama] bin Laden in Afghanistan and discussed the operational concept of hijacking commercial airliners and crashing them into buildings in the United States and elsewhere. This plan was ultimately approved by [Osama] bin Laden.”

The charges against Mohammed and the other four co-conspirators include murder, hijacking and terrorism.