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.

“There is no evidence that these defendants personally maimed, kidnapped or killed anyone in the United States or elsewhere,” Judge Cooke said. “There was never a plot to overthrow the United States government.”

Back in 2002, a master’s degree candidate at the Naval War College wrote a paper on the Bush administration’s plan to use military commissions to try Guantánamo suspects, concluding that “even a good military tribunal is a bad idea.” It drew little notice at the time, but the paper has gained a second life because of its author’s big promotion: Col. Ralph H. Kohlmann of the Marines is now the chief judge of the military commissions at the naval base in Guantánamo Bay, Cuba.