Khaled Sheikh Mohammed was one of five men who appeared in public for the first time in years at the start of a US military hearing at the Guantanamo Bay base.
Sheikh Mohammed, a Pakistani, and his alleged co-conspirators Ramzi Binalshibh , Ali Abd al-Aziz Ali, Wallid bin Attash and Mustapha al-Hawsawi all face the death penalty if convicted by the military commission on the US base on Cuba.
Charges against them include conspiracy, murder, attacking civilians, intentionally causing serious bodily injury, destruction of property, terrorism, and material support for terrorism.
The men appeared relaxed as they chatted in Arabic, waiting for the hearing to begin at which the charges will be read against to them by judge Colonel Ralph Kohlmann.
The judge opened the military commission by saying the government would consider any statements by the five as confidential because of their detentions in secret CIA prisons.
"Any statement by any of the detainees is presumptively classified," Kohlmann said.
That means there was to be a 20-second delay before the defendants statements are broadcast by video to the nearby purpose-built press room in order to allow prosecutors to cut any sensitive information.
The five will get the chance on Thursday to say if they accept their military and civilian defense lawyers, and whether they wish to plead immediately on the charges.
All the suspects were arrested between 2002 and 2003, and transferred to the controversial base on Cuba in 2006, allegedly after spending years in secret CIA prisons.
Sheikh Mohammed, 43, has claimed to have been behind not just the September 11 attacks but also some 30 operations against the West in the past decade, according to transcripts of his interrogation released by the Pentagon.
His appearance on Thursday is the first time he has been seen in public since his capture in Pakistan on March 1, 2003.
The military tribunals have been mired in controversy since they were established by President George W. Bush at the end of 2001.
In 2006, the US Supreme Court ruled they were illegal, but then Congress adopted a new law allowing for them to be re-established and allowing indirect witness statements or testimony won under duress to be submitted as evidence.
Brigadier General Thomas Hartmann, legal advisor to the military commissions, said the defense team had been granted "extraordinary" rights.
But he noted that if they are acquitted, the suspects could still continue to be held until the end of the so-called "war on terror."
"This is a fundamentally flawed process and we will zealously identify and expose each and every one (of its flaws). Our nation deserves better than this," countered chief defense counsel Colonel Steven David.
A village of tents has been set up on an old landing strip to accommodate the journalists and other visitors who have traveled to Cuba for the hearing.