Military prosecutors are in the final phases of preparing the first sweeping case against suspected conspirators in the plot that led to the deaths of nearly 3,000 Americans on Sept. 11, 2001, and drew the United States into war, people who have been briefed on the case said.
The charges, to be filed in the military commission system at Guantánamo Bay, Cuba, would involve as many as six detainees held at the detention camp, including Khalid Shaikh Mohammed, the former senior aide to Osama bin Laden, who has said he was the principal planner of the plot.
The case could begin to fulfill a longtime goal of the Bush administration: establishing culpability for the terrorist attacks of 2001. It could also help the administration make its case that some detainees at Guantánamo, where 275 men remain, would pose a threat if they are not held at Guantánamo or elsewhere. Officials have long said that a half-dozen men held at Guantánamo played essential roles in the plot directed by Mr. Mohammed, from would-be hijackers to financiers.
But the case would also bring new scrutiny to the military commission system, which has a troubled history and has been criticized as a system designed to win convictions but that does not provide the legal protections of American civilian courts.
The Military Tribunal courtroom.
Military prosecutors at the Guantanamo Bay detention camp announced charges on Monday against six captives they claim were involved in the planning of the September 11 attacks. The men, each facing the death penalty, will be tried in a single group.

The move could cause legal problems, since the Bush Administration has admitted that at some of the confessions were given under torture. In 2006, a source in the Pentagon referred to several of the captives now facing prosecution as "unprosecutable" due to "the techniques" used to secure their confessions.

The administration confirmed last week that Khalid 
Sheikh Mohammed had been subjected to waterboarding - which it defines as an "Enhanced interrogation technique". The alleged planner of the September 11 attacks confessed to planning a number of other crimes. Included in his list of confessions were the failed shoe-bombing in England and 1993 bombing of the World Trade Centre, trying to assassinate Jimmy Carter, Bill Clinton, Pervez Musharraf and Pope John Paul II, the beheading of reporter Daniel Pearl in Pakistan, the Nightclub bombing in Bali, plots against oil tankers in Singapore and an oil company owned by Henry Kissinger, plans to blow up the Panama Canal, Heathrow Airport, the Sear Towers in Chicago, the Empire State Building in New York and the Library Tower in Los Angeles, attacks against a number of nightclubs in Thailand, shooting down an Israeli plane, destroying suspension bridges and bombing a hotel in Kenya and targets in South Korea. He also confessed to attacks and plots in Kuwait, Australia, Turkey, Japan, South Korea and Indonesia. William Glaberson of ''The New York Times'' has suggested that the willingness to confess to every accusation presented against him might make it more difficult for prosecutors to establish the validity of his confessions.

Mohamed al-Kahtani, one of sixteen people accused of being a "20th hijacker", has recanted his confessions that he had ties to Al Qaeda, had been sent to serve as a hijacker, and that he recognised thirty other captives as bodyguards of Osama bin Laden. He has stated that he was tortured and his family was threatened - in order to force his confessions. A copy of his interrogation log documented that he had been subjected to almost two months of continuous sleep deprivation, with three shifts of interrogators working around the clock to keep him disoriented.  His interrogation log documents that he was bound to chairs and force-fed, and administered enemas and IVs, in order to keep his body functioning during his extended sessions..

Walid bin 'Attash faces charges that he helped run a training camp in Lowgar, Afghanistan that trained two of the hijackers, and that he observed airport security during a flight to Malaysia, to aid the hijackers.

Ramzi Binalshibh is accused of helping the attackers enroll in American flight schools, been in frequent communication with them helped finance their time in the United States.

Ali Abdul Aziz Ali is alleged to have helped finance the hijackers' stay in the United States, teaching them to find hotels, use travellers' cheques and fit into Western culture.

Mustafa al-Hawsawi, originally thought to be another alias of Ali's, is likewise accused of helping the hijackers buy Western clothing, sign up for credit cards and financing their stay before the attacks.

The charges will be referred to Susan J. Crawford, appointed the convening authority of the Guantanamo military commissions last year, to determine if there is probable cause for proceedings to continue.

The commissions were established in 2006, after the Supreme Court ruled in Hamdan v. Rumsfeld that the system of tribunals was illegal, violating both International and American laws designed to ensure the fair treatment and trials of captives. The tribunals have been criticized for only being used against a handful of detainees, and not reaching a verdict on any of the cases.