GWEN IFILL: Finally tonight, a legal proceeding against the mastermind of the 9/11 attacks and four others.
Margaret Warner has the story.
MARGARET WARNER: Saturday marked the first court appearance in more than three years for Khalid Sheikh Mohammed. The self-professed mastermind of the 9/11 attacks and four co-defendants were arraigned before a military court at Guantanamo Bay, Cuba.
The men made a concerted attempt to disrupt the session which ran 13 hours.
James Connell, one of the defense attorneys, said Sunday they are victims of an unjust system.
JAMES CONNELL, defense attorney: These men have endured years of inhumane treatment and torture. This serious -- this treatment has had serious long-term effects and will ultimately infect every aspect of this military commission tribunal.
MARGARET WARNER: Indeed, Khalid Sheikh Mohammed, often referred to as KSM, was captured in Pakistan in March of 2003 and was held in secret CIA prisons for three years, before being transferred to Guantanamo in 2006.
The government has acknowledged he was water-boarded 183 times in 2003, before the practice was banned. On Friday, the lead prosecutor, Brigadier General Mark Martins, insisted whatever came of such sessions won't find its way into court.
BRIG. GEN. MARK MARTINS, chief U.S. Army prosecutor: The law prohibits the use of any statement obtained as the result of torture or cruel, inhuman or degrading treatment, and we will implement the law.
SPENCER MICHELS: Mohammed's co-defendants, Ramzi Binalshibh, charged with finding flight schools and helping the hijackers enter the U.S., Waleed Bin Attash, who allegedly ran a camp where two of the 9/11 hijackers trained, and Mustafa Ahmed al-Hawsawi and Ali Abd al-Aziz, both accused of providing the 9/11 attackers with money, clothing, credit cards and travel arrangements.
Each man is charged with 2,976 counts of murder and terrorism and potentially faces the death penalty. Six family members of 9/11 victims were chosen by lottery to attend Saturday's proceedings at Guantanamo, seated behind glass.
EDWARD BRACKEN, brother of 9/11 Victim: I'm going to see the people that killed my sister face to face. And that's what you do in America. You go and you face your fight. And that's what we do. And, you know, we bring people to justice.
MARGARET WARNER: The Bush administration began prosecuting the men in the military justice system in 2008. But a year later, President Obama's attorney general, Eric Holder, announced they'd be tried in federal court in Lower Manhattan, just blocks from the World Trade Center. That plan was scrapped amid security fears and a political uproar.