The four other defendants are all accused of being Mohammed's underlings and playing more minor roles in the attacks, such as providing money and other assistance to the hijackers.
All five face the same charges, including conspiracy, attacking civilians, terrorism and 2,976 counts of murder in violation of the law of war, one for each official victim of the Sept. 11 attacks at the time the charges were filed. Each of the men could get the death penalty if convicted.
What has happened so far?
The five were arraigned in May at the U.S. base in Cuba in a sometimes-unruly 13-hour hearing in which the men appeared to make a concerted effort to delay the proceeding by refusing to respond to questions from the military judge or use the court's translation system to follow the proceedings in Arabic. They didn't enter a plea, though Mohammed in the past has indicated he wanted to plead guilty.
Since then, prosecutors and defense lawyers have filed dozens of pretrial motions dealing with a wide range of legal issues, such as the rules for handling classified evidence or what clothing the defendants will be allowed to wear in court. The judge must hold pretrial hearings on many of the motions, but those have been delayed by the challenge of scheduling court appearances for all the attorneys and prosecutors involved in the case, a break for the Muslim holy period of Ramadan, and Tropical Storm Isaac, which forced the military to cancel several days of hearings in August. The government has scheduled another round of pretrial hearings to start Oct. 15.
But there is a long way to go. Many of the unresolved issues are preliminary, and defense lawyers say they have not even received much of the evidence against their clients. If this were a football game, they'd still be on the coin toss.
Why is it taking so long to try them?
The men, all of whom were held in secret CIA "black sites" before being taken to Guantanamo in September 2006, were arraigned the first time in June 2008, a process that was delayed by legal challenges to the military commissions. After that first arraignment, the case bogged down in pretrial hearings until the election of President Barack Obama, who put the case on hold while he tried to move the case to a civilian court in the U.S. as part of a broader plan to close the Guantanamo Bay prison.
Members of Congress opposed holding the case in New York City, or anywhere in the U.S., and blocked the administration from moving any prisoners to the U.S. So the government sent it back to a military commission system that has since been reformed to address criticism that the tribunals were unfair and would allow the use of evidence tainted by harsh treatment that critics call torture.
What happens next?
There are hundreds of motions to be litigated at pretrial hearings. There's no trial date. One defense lawyer recently predicted the trial is about four years away. The chief military prosecutor, Army Brig. Gen. Mark Martins, has said only that it is "many months" off.
If and when there's a verdict, it must be reviewed and approved by a Pentagon-legal official known as the Convening Authority. Then, the defendants can appeal to the Court of Military Commission Review, followed by the Court of Appeals for the D.C. Circuit and finally to the Supreme Court. The military has not said how it would carry out any executions.