This time the defendants may put up a fight.
Khalid Sheikh Mohammed, who told military authorities that he was responsible for the planning of the terror assault "from A to Z," previously mocked the tribunal and said he would welcome the death penalty. His co-defendant, Ramzi Binalshibh, told the court that he was proud of the attacks.
But Jim Harrington, the civilian lawyer for Binalshibh, said the defendants are expected to fight the charges against them, which include murder and terrorism and carry a potential death penalty.
"He has no intention of pleading guilty," Harrington said. "I don't think anyone is going to plead guilty." Harrington declined to say what would be the basis of his defense and lawyers for Mohammed did not respond to messages seeking comment.
The men never entered formal pleas in previous hearings, but Mohammed told the court that he would confess to planning the attacks and hoped to be a "martyr." He dismissed the military justice system, saying, "After torturing, they transferred us to inquisition land in Guantanamo."
Now after three years in which the tribunals known as military commissions have been reformed by Congress and the president, they've had time to reconsider their defense.
"I'm not sure they really understood the ramifications of it at that time," Harrington said.
The arraignment Saturday, before an audience that includes a handful of people who lost family members in the Sept. 11 attacks as well as journalists and human rights observers, will be followed by a hearing on a series of defense motions that challenge the charges and the extreme secrecy rules imposed to prevent the release of information about U.S. counterterrorism methods and strategy. The start of their actual trial is at least a year away.
The five defendants are held in a section of Guantanamo that is under such tight security even its exact location on the base is classified, a prison-within-a-prison known as Camp 7. They have not been seen in public since the day after Obama's inauguration, when the commission held a hearing to continue their case.
New rules adopted by Congress and Obama forbid the use of testimony obtained through cruel treatment or torture. The defendants were held at secret CIA prisons overseas where they were subjected to what the government called "enhanced interrogation techniques." Mohammed was waterboarded 183 times, officials have said.
Critics such as Kenneth Roth, executive director of Human Rights Watch and a former federal prosecutor, say coerced testimony from witnesses is still admissible, even if it isn't from defendants, and the case would be better off in civilian court instead of being heard by a judge and jury panel picked by the Pentagon.
"There still are major problems in terms of whether the trial will be fair and, more important, will they be perceived as fair," Roth said.
The government has also pledged to make the proceedings more transparent, broadcasting hearings to several U.S. military bases in the Northeast so the families of Sept. 11 victims can monitor the trial without making the trek to Guantanamo.
News cameras, however, are still not permitted inside the courtroom, where the media and other observers are kept behind double-paned, soundproof glass. Lawyers for the defendants had opposed the government's plan to show the hearings by closed-circuit TV to bases in the U.S., arguing that they should be broadcast to everyone.
"We believe that the world needs to see what's happening," said Cheryl Bormann, a civilian attorney appointed to represent defendant Walid bin 'Attash.
Prisoners now have access, at government expense, to civilian defense attorneys who specialize in complex death penalty cases. But human rights groups and defense lawyers still condemn the proceedings as flawed and fundamentally unfair.
Lawyers appointed to represent the men say they face hurdles they would never encounter in a civilian court, including strict limits on what they can say about their clients, whose every utterance is treated as presumptively classified. Courtroom proceedings are subject to a 45-second delay so censors can prevent the inadvertent disclosure of government secrets, a system that critics say is intended merely to prevent anyone from learning details about the men's treatment.
"All I can do is try and protect my client's rights to every extent I can and try and hold the government to their burden to provide a fair and transparent justice system and to actually mean it," Bormann said.
Mohammed and his co-defendants were first arraigned on the U.S. base in Cuba in June 2008. The case quickly bogged down in pretrial motions and was put on hold as Obama sought to move the case to the federal court in New York.
But members of Congress balked and blocked the administration from transferring prisoners from the base to the mainland. That prevented the closure of the prison, where the U.S. still holds 169 prisoners.
One of the biggest differences between the previous hearing and this hearing is that there is no doubt that they will be tried by a military tribunal.
"There is a consensus now ... that military commissions have a narrow but critical role in our counterterrorism and justice system," said Brig. Gen. Mark Martins, a Harvard Law School classmate of Obama's who was appointed chief prosecutor last year.
Mohammed, a Pakistani citizen who grew up in Kuwait and attended college in Greensboro, North Carolina, confessed to military authorities that he planned or carried out about 30 plots around the world. He admitted personally killing Wall Street Journal reporter Daniel Pearl and said he conceived the plot to blow up a trans-Atlantic flight by would-be shoe-bomber Richard Reid in 2001. Mohammed was captured in 2003 in Pakistan.
His four co-defendants are accused of support roles in the Sept. 11 attacks: Binalshibh, a Yemeni, was allegedly chosen to be a hijacker but couldn't get a U.S. visa and ended up providing assistance such as finding flight schools; Waleed bin Attash, also from Yemen, allegedly ran an al-Qaida training camp in Afghanistan and researched flight simulators and timetables; Mustafa Ahmad al-Hawsawi, a Saudi accused of helping the hijackers with money, Western clothing, traveler's checks and credit cards; Ali Abd al-Aziz Ali, a Pakistani national and nephew of KSM, allegedly provided money to the hijackers.
All five face charges that include 2,976 counts of murder, one for each person killed in the Sept. 11 plot that sent hijacked commercial airliners slamming into New York's World Trade Center, the Pentagon and a field in Shanksville, Pennsylvania.
Human rights groups and many members of the legal community say the reforms have not gone far enough and the only legitimate way to prosecute Mohammed is in a civilian court, not a commission with a jury of Pentagon-appointed military officers and an Army colonel for a judge.
Roth, who will be part of a human rights contingent observing Saturday's arraignment at Guantanamo, said the prosecution can work around the ban on coerced testimony, perhaps even unwittingly, by introducing classified summaries of intelligence to support their case.
Even with the changes, the defense lawyers say the commissions are anything but fair. They complain that their mail is improperly reviewed by the military, interfering with attorney-client privilege, that they aren't given enough resources to investigate cases the government spent years building, that too many hearings are still held in secret and that they are barred from disclosing anything their clients tell them.
"You can take a $5 mule and put a $10,000 saddle on it and call it reformed," said Navy Cmdr. Walter Ruiz, a military lawyer for Saudi defendant al-Hawsawi. "You still have a $5 mule; it just has a fancy saddle."