Khalid Sheikh Mohammed and four suspected co-conspirators were ordered on Wednesday to stand trial before a Guantanamo war crimes tribunal, accused of organising the September 11 attacks of 2001, the Pentagon said.
It is a move that throws the politically charged case into the limelight in an election year.
Convictions on the most serious charges, which include terrorism, hijacking, conspiracy and murder in violation of the law of war, could carry the death penalty.
The decision to move to trial in a military court is the latest chapter in a decade-long political and legal battle over handling detainees. One of the most contentious issues has been whether terrorism suspects like Mohammed and his alleged co-conspirators should be tried in civilian courts as criminals or before military courts as enemy combatants.
The trial will bring a deep examination of the events leading up to 9/11, the deadliest attack ever carried out on U.S. soil and one that propelled the country into a global war against al Qaeda and its affiliates.
The trial stands to be double-edged for President Barack Obama, who is running for a second term in November. It will remind voters about the killing of long-fugitive al Qaeda leader Osama bin Laden last year, a highlight of his presidency. But it could also draw attention to his failure to close the Guantanamo Bay prison, which he had promised to do as a candidate in the 2008 election.
The official overseeing the Guantanamo tribunals, retired Vice Admiral Bruce MacDonald, referred the case to a capital military commission on charges of terrorism, hijacking aircraft, conspiracy, murder in violation of the law of war, attacking civilians and other counts, the Pentagon said.
The case is fraught with controversy. All five defendants were held in secret CIA prisons before being sent to Guantanamo in 2006. The CIA has acknowledged subjecting Mohammed to a simulated drowning technique known as waterboarding during his interrogation, and other defendants have said they were abused.
The tribunals, which have gone through several revisions, ban the use of evidence gained through coercion, but critics say the hearsay rules are broad enough to allow the introduction of second-hand information obtained through torture.
Asked on Wednesday about the decision to proceed to trial, White House spokesman Jay Carney said, "It has been more than 10 years since 9/11 ... and the president is committed to ensuring that those who were accused of perpetrating the attacks against the United States be brought to justice."
Carney said Obama remained committed to closing the U.S. military facility in Cuba that houses high-risk terrorist suspects, blaming its continued operation on "obstacles ... from Congress."
The prison at Guantanamo still holds 171 people, down from 252 when Obama took office. The president had promised to close the facility by the end of his first year in office, but the deadline passed as the administration struggled against the hard reality of finding other countries willing to take the inmates.
Mohammed, who is Pakistani, and the other four are accused of planning and executing the Sept. 11, 2001, hijacked airliner attacks that killed 2,976 people in New York, Washington and Shanksville, Pennsylvania. The attacks were part of a conspiracy involving al Qaeda leader Osama bin Laden and other members of his group.
The five were initially charged in the Guantanamo war crimes court in 2008. Obama, then a candidate for president, opposed the use of the tribunals. After his election, Attorney General Eric Holder moved to have the case transferred to a federal court in New York and the military charges were dropped.
The effort to try the case in civilian court ran into stiff resistance in Congress and in New York, where officials warned about the security threat and said the cost of protecting the venue could be as much as $1 billion. Congress eventually blocked the transfer of Guantanamo prisoners to the United States for trial or any other reason.
One year ago, on April 4, 2011, the administration abandoned efforts to try the case before a civilian court near the site of the World Trade Center attack, as Obama had promised, and shifted the case back to a military tribunal at Guantanamo.
Holder blamed lawmakers for the policy reversal, saying their decision to block funding for prosecuting the Sept. 11 suspects in a New York court had forced the administration to move back to a military trial.
Representative Buck McKeon, Republican chairman of the House Armed Services Committee, welcomed the decision to try the group before a military commission at Guantanamo, saying it was time for "judgment to be passed and long-delayed justice to be done."
The American Civil Liberties Union condemned Wednesday's decision to proceed with a military case, saying the administration was "making a terrible mistake by prosecuting the most important terrorism trials of our time in a second-tier system of justice."
"Whatever verdict comes out of the Guantanamo military commissions will be tainted by an unfair process and the politics that wrongly pulled these cases from federal courts, which have safely and successfully handled hundreds of terrorism trials," ACLU Executive Director Anthony Romero said.
The decision to refer the case to a tribunal means the five will have to be arraigned before a military judge at Guantanamo within 30 days of their formal notification that the case will go to trial. Notification is expected to happen on Thursday, a Pentagon spokesman said.
The case has been referred to a joint trial, meaning the five will be tried together. In addition to Mohammed, the accused are Walid bin Attash, Ramzi Binalshibh, Ali Abdul Aziz Ali and Mustafa Ahmed al Hawsawi.
James Connell, the civilian attorney for Aziz Ali, said in a statement that his client, a nephew of Mohammed, did not kill or plan to kill anyone and should not face the death penalty.
Ali's attorneys have said in the past that he was a computer worker in Dubai who sent money to the hijackers and was not a direct participant in planning the attacks.
"Mr. Ali would not be eligible for the death penalty if this case were tried in federal court," Connell said. "This attempt to expand the reach of the death penalty to people who neither killed nor planned to kill is another example of the second-class justice of the military commissions."