That effort collapsed in the face of congressional and local opposition. In April 2011, Attorney General Eric H. Holder Jr. announced that he was reluctantly sending the case back to the military.
Military charges against the five men were re-sworn in June. And on Wednesday, retired Vice Adm. Bruce MacDonald, the official who oversees the commissions and is known as the convening authority, sent the case for trial after reviewing and approving those charges.
They include murder in violation of the law of war, attacking civilians, attacking civilian objects, hijacking aircraft and terrorism. If convicted, the men could face the death penalty.
Charged along with Mohammed are Ali Abdul Aziz Ali, a Pakistani who is Mohammed’s nephew; Ramzi Binalshibh and Walid bin Attash, both Yemenis; and Mustafa al-Hawsawi, a Saudi. All are accused of playing key organizational or financial roles in the attacks on New York and the Pentagon, a plot that Mohammed has said he masterminded.
In the previous case, Mohammed, Ali and Attash won the right to represent themselves with advisory military and civilian counsel. A judge was considering whether Binalshibh and Hawsawi were competent to make that choice when the case was suspended.
An arraignment will be held at the military prison at Guantanamo Bay next month, and all of the pretrial issues that surfaced in the earlier case will have to be litigated again, including the issue of self-representation and the mental health and capacity of Binalshibh and Hawsawi.
Each of the defendants is entitled to a military attorney and “learned counsel,” a lawyer with experience in death penalty cases.
At one point in the last case, the defendants said they were interested in pleading guilty to capital charges because they wanted to be executed and die as martyrs. Next month’s arraignment should make clear whether Mohammed wants to fight the charges or is still interested in pleading guilty.
The other defendants have tended to follow his lead.
All five men were held in secret CIA custody at prisons overseas before they were transferred to Guantanamo in September 2006. Their treatment at the hands of the CIA, including the extensive waterboarding of Mohammed, is likely to be an issue at trial.
Under the reformed system of military commissions, prosecutors cannot use as evidence any statement that resulted from torture or cruel, inhumane or degrading treatment. Attorneys for the men are nonetheless likely to make their treatment central to any defense against the death penalty.
Some civil libertarians remain deeply skeptical of the system.
“The military commissions were set up to achieve easy convictions and hide the reality of torture, not to provide a fair trial,” said Anthony D. Romero, executive director of the ACLU. “Although the rules have been improved, the military commissions continue to violate due process by allowing the use of hearsay and coerced or secret evidence.”
But military officials said the commissions, which were overhauled in 2009 by Congress, offer defendants due process. They also said the use of hearsay or coerced evidence is strictly limited to certain circumstances on the battlefield and is not a back door for tainted evidence.
“If observers withhold judgment for a time, the system they see will prove itself deserving of public confidence,” Brig. Gen. Mark Martins, the chief military prosecutor at Guantanamo Bay, said in a speech this week at Harvard Law School.