Brig. Gen. Thomas W. Hartmann, the legal adviser to the tribunal system, announced that 169 charges had been sworn against six men "alleged to be responsible for the planning and execution of the attacks" in 2001 that killed nearly 3,000 people.
"These charges allege a long-term, highly sophisticated, organized plan by al-Qaida to attack the United States of America," Hartmann told a Pentagon press conference.
Officials said they'll seek the death penalty and hope to try all six together. That would make it the first capital trial under the terrorism-era military tribunal system.
Hartmann said the six include Khalid Sheikh Mohammed, the suspected mastermind of the attacks in which hijackers flew planes into buildings in New York and Washington. Another hijacked plane crashed in the fields of western Pennsylvania.
The other five men being charged are: Mohammed al-Qahtani, who officials have labeled the 20th hijacker; Ramzi Binalshibh, said to have been the main intermediary between the hijackers and al-Qaida leaders; Ali Abd al-Aziz Ali, known as Ammar al-Baluchi, a nephew and lieutenant of Khalid Sheikh Mohammed; al-Baluchi's assistant, Mustafa Ahmad al-Hawsawi; and Waleed bin Attash, a detainee known as Khallad, who investigators say selected and trained some of the 19 hijackers.
Dominic J. Puopolo Jr., whose mother, Sonia Morales Puopolo, was a passenger aboard one of the downed airliners, said he was relieved but had mixed feelings.
"There's a feeling that we have to rehash this again and it will be in the media and bring back some very painful memories," he said. "On the other hand, the worst of the worst are going to be held accountable for their actions."
Asked what impact it will have on the case that Mohammed was subjected to waterboarding by CIA interrogators, Hartmann said it will be up to the tribunal judge to determine what evidence is allowed.
Al-Qahtani also has alleged torture and last fall recanted a confession he said he made after he was beaten, abused and humiliated at Guantanamo. Officials have acknowledged that he was subjected to harsh treatment at the prison authorized by former Defense Secretary Donald H. Rumsfeld.
The Center for Constitutional Rights, which represents al-Qahtani, called the tribunals "a perversion of justice" and "morally reprehensible system."
Prosecutors have been working for years to assemble the case against suspects in the attacks that prompted the Bush administration to launch the global war on terror.
The men would be tried in the military tribunal system that was set up by the administration shortly after the start of the counterterror war. That system has been widely criticized for its rules on legal representation for suspects, hearings behind closed doors and past allegations of inmate abuse at Guantanamo.
Original rules allowed the military to exclude defendants from their own trials, permitted statements made under torture, and forbade appeal to an independent court; but the U.S. Supreme Court struck down the system in 2006 and a revised plan set up after Congress enacted a new law has included some additional rights.
Defense lawyers still criticize the system for its secrecy.
But Hartmann said Monday that the defendants will get the same rights as U.S. soldiers tried under the military justice system including the right to remain silent, call witnesses, and know the evidence against them. Appeals can go all the way to the Supreme Court.
He called the charges sworn Monday "only allegations" and said the accused will remain innocent until proven guilty.
The decision to seek the death penalty also is likely to draw criticism from the international community. A number of countries, including U.S. allies, have said they would object to the use of capital punishment for their nationals held at Guantanamo.
The U.S. government unsuccessfully sought the death penalty in its only civilian trial of charges related to Sept. 11. In that case, Zacarias Moussaoui, who was behind bars in Minnesota on 9/11, was sentenced to life in prison.
Glenn Sulmasy, a national security fellow at Harvard and a supporter of military commissions, acknowledged the tribunal system's early problems created cynicism and skepticism, particularly among international observers.
"We have to recognize this is new. It's a hybrid war, a hybrid warrior and we need a hybrid court," Sulmasy said. "To be overly critical is unfortunate and unnecessary for the international community."
He noted the terrorism trial could stretch into the next president's administration and said it's also possible the Supreme Court will again strike down the military commissions law and force yet another change.
The military tribunal system requires that a panel of 12 unanimously find a defendant guilty for capital punishment cases, Hartmann said.
Officials plan to hold the trial in a specially constructed court at Guantanamo that will allow lawyers, journalists and some others to be present, but leave relatives of Sept. 11 victims and others to watch the trial through closed-circuit broadcasts.
Asked where an execution might take place, Hartmann said: "We are a long way from determining the details of the death penalty. And when that time comes, if it should ever come at all, we will follow the law at that time and the procedures that are in place at that time."
Mohammed was among 15 so-called "high-value detainees" who were held at length by the CIA in secret overseas prisons -- some subjected to what critics call torture -- before being handed over to the military in 2006.
Last week, for the first time, the administration acknowledged that Mohammed was among three suspects who were waterboarded. CIA Director Michael Hayden said the tactic was used, in part, because of widespread belief among U.S. intelligence officials that more catastrophic attacks were imminent.
Waterboarding involves strapping a person down and pouring water over the suspect's cloth-covered face to create the sensation of drowning. It has been traced back hundreds of years, to the Spanish Inquisition, and is condemned by nations around the world.
In Guantanamo Bay hearings that have been criticized as unfair, Mohammed in March confessed to the 9/11 attack, the beheading of American journalist Daniel Pearl and a chilling string of other terror plots.
"I was responsible for the 9/11 operation from A to Z," Mohammed said in a statement read during the session, according to hearing transcripts later released by the Pentagon.
Under the tribunal system, the charges are forwarded to the convening authority, who can refer some or all of them for trial.
It could be months or longer before trials begin for the defendants. With the appeals process, it would likely be some time after any convictions before executions would be possible.
White House press secretary Dana Perino said Monday that President Bush and the White House had no role in the decision to seek the death penalty for the six charged.
"Obviously 9-11 was a defining moment in our history, and a defining moment in the global war on terror," Perino said. "And this judicial process is the next step in that story. The president is sure that the military is going to follow through in a way that the Congress said they should."
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