The accused men, one of whom was brought to the arraignment hearing strapped to a restraining chair after refusing to attend, dropped their previous insistence on pleading guilty and demanding to be executed in favour of largely sitting in silence as defence lawyers attempted to raise the issue of torture and question the independence of the judge.
None of the defendants chose to enter a plea at the hearing and reserved it for a later appearance. The judge set a tentative trial date of May 2013 although he acknowledged that there are likely to be more delays. After a 13-hour session to arraign the suspects, proceedings have been adjourned until 12 June.
Mohammed's lawyer, David Nevin, told the court that "the world is watching" the trial after the US government admitted to waterboarding the accused terrorist 183 times. Another defence lawyer, James Connell, called the military tribunal a "blight on America's international reputation and her commitment to the rule of law".
Mohammed and his co-accused - Ramzi bin al-Shibh, Ali Abd al-Aziz Ali, Mustafa Ahmed al-Hawsawi and Walid bin Attash - each face 2,976 counts of murder representing the victims who died on 9/11, as well as accusations of terrorism, hijacking, conspiracy and destruction of property. The prosecution is seeking the death penalty for all of the men.
At an arraignment hearing in 2008 Mohammed mocked the court and tried to plead guilty, saying he wanted to be put to death as a martyr. The US supreme court later struck down the rules of evidence and the trial was called off.
Mohammed has previously compared himself to George Washington and demanded to be treated as a combatant, not a terrorist.
In contrast on Saturday the accused men refused to participate in the one-day hearing. Early in the proceedings the accused removed their headphones used for translation. Nevin said that in Mohammed's case it was because of his treatment while under interrogation by the Central Intelligence Agency. "The reason he's not putting the headphones in his ears is because of the torture imposed on him," he said.
Nevin asked to be allowed to elaborate but the judge, Colonel James Pohl, refused.
Pohl said that if the men refused to participate in proceedings then in due course a plea of not guilty would be entered on their behalf. "One cannot choose not to participate and frustrate the normal course of business," he said.
The issue of torture has badly tainted the military tribunal, which is the second attempt to put the men on trial after the US supreme court blocked an earlier prosecution over protection of the accused's rights.
The chief military prosecutor, Brigadier General Mark Martins, urged critics to give the tribunal a chance. "I'm confident that this court can achieve justice and fairness," he said. "This is a system worthy of the nation's confidence."
The accused men generally sat quietly, dressed entirely in white clothes and turbans they were required to wear by their military jailers. But Bin al-Shibh briefly interrupted proceedings by shouting and comparing the Guantánamo prison to life under the former Libyan dictator, Muammar Gaddafi. "Era of Gaddafi is over but you have Gaddafi in [Guantánamo] camp. Maybe they are going to kill us and say that we are committing suicide," he said.
Most of the disruption was procedural and came from the defence lawyers who conducted what appeared to be a co-ordinated and lengthy challenge to the credibility of the court and Pohl's independence that dragged on for much of the day.
Nevin sought to suggest that the judge could not oversee the trial of men who were the enemies of the military he serves. Pohl acknowledged that he served in Afghanistan and Iraq, occasionally came under indirect fire and knew fellow soldiers killed in combat, although not well. He said this would not affect his judgment.
Nevin pressed on, suggesting to Pohl that he could not be a neutral arbiter as part of the US military fighting the people being judged. Pohl responded that if that were the case no military court could try the men. "Exactly!" said Nevin.
The only female defence lawyer, Cheryl Bormann, asked the judge to order women members of the prosecution, who were wearing skirts, to cover themselves up "so that our clients are not forced to not look at the prosecution for fear of committing a sin under their faith". Bormann was wearing an abaya - an Islamic women's robe revealing only the face, hands and feet.
Relatives of those who died in the 9/11 attacks welcomed the fact that more than a decade later the organisers are finally to face justice. Among the relatives of the dead watching the proceedings at Guantánamo was Cliff Russell, whose brother, a firefighter, was killed in the World Trade Centre.
"I wish the worst possible death for them," he said. "I'm not looking forward to ending someone else's life and taking satisfaction in it, but it's the most disgusting, hateful, awful thing I ever could think of if you think about what was perpetrated."
Tara Henwood Butzbaugh, whose brother was working on the 105th floor of one of the towers when the planes hit, echoed the call. "Death," she said. "Nothing less."
Comment: Cliff Russel and Tara Henwood Butzbaugh are looking in the wrong direction for the perpetrators:
Mossad and Moving Companies: Masterminds of Global Terrorism
But Blake Allison, whose wife was on the first plane to hit the towers, said he was opposed to the death penalty for the accused men. "It's not a productive or appropriate way to resolve something," he said. "It just perpetuates the idea of needing revenge."
Defence lawyers promised a lengthy fight. "This is only the beginning of a trial that will take years to complete, followed by years of appellate review," said Connell. "I can't imagine any scenario where this thing gets wrapped up in six months."
Some people can't find a job with one or more scientific university degrees while CIA psychopaths earn their salaries by torturing human beings as a "normal" workday task. Damned planet indeed.