WASHINGTON — In April 2001, seven months after the Navy destroyer Cole was bombed in Yemen, Abd al-Rahim al-Nashiri was staying at a Qaeda guesthouse in Afghanistan when he is alleged to have laid out how he had planned the whole thing.
Attorney General Eric H. Holder Jr. decided a military commission would prosecute Mr. Nashiri.
One of those houseguests was later captured, and he told F.B.I. agents the story of those boasts and implied that he could be a star witness if Mr. Nashiri were tried for the murder of the 17 American sailors killed in the attack.
That trial is going to happen, but that witness is no longer available. Still, prosecutors may not need him. Mr. Nashiri will be tried by a military commission, and under the rules there, F.B.I. agents can simply repeat the accounts of witnesses — indirect testimony that would generally be inadmissible in a civilian court.
Mr. Nashiri’s case will be the marquee test of a new tribunal system designed to handle terrorism suspects. But the decision by Attorney General Eric H. Holder Jr. to prosecute him before a commission, while putting the self-proclaimed mastermind of the Sept. 11 attacks, Khalid Shaikh Mohammed, before a civilian court, has set off a fierce debate.
Some conservatives have argued that all accused terrorists should be tried before commissions, like the one that will decide Mr. Nashiri’s fate. It is too risky, they contend, to try any terror defendant in the civilian legal system, where the rules of evidence are far more restrictive.
Civil libertarians, on the other hand, contend that the administration’s approach amounts to a two-tier system in which cases with weaker evidence receive second-class justice by being shunted into the looser commission system.
A close look at the evidence against Mr. Nashiri provides a case study of the significant differences that remain between civilian trials and military commissions, even after a recent overhaul by Congress. It shows that it would indeed be simpler to introduce certain evidence against terror defendants in commissions, but that nagging questions about the legality of the military court system present significant hurdles.
A review of public documents and interviews with current and former officials familiar with the case also illuminates the difficult trade-offs the administration faces as it pores through the prison population at Guantánamo Bay, Cuba, and decides the fates of detainees like Mr. Mohammed and Mr. Nashiri.
In explaining why Mr. Nashiri would not receive a civilian trial, Mr. Holder cited “a variety of factors” while emphasizing one in particular: It “was an attack on a United States warship, and that, I think, is appropriately placed into the military commissions setting.”
But several current and former officials familiar with the case say that concerns about the evidence against Mr. Nashiri were an overriding factor. Prosecuting him under the more stringent rules of civilian court would have been perilous. Most of that evidence consists of hearsay — statements made outside court, like the former detainee’s account of what he said he heard Mr. Nashiri say in April 2001.
In a civilian trial, hearsay statements generally cannot be introduced because there is no opportunity for defense lawyers to cross-examine the witness. But under commission rules, F.B.I. agents could tell a military jury what Mr. Nashiri told the detainee, according to the detainee.
“In a federal court where the Constitution applies, a defendant is allowed to confront his accusers face to face,” said Lt. Cmdr. Stephen Reyes of the Navy, the military lawyer assigned to represent Mr. Nashiri. “In this case, Nashiri could be convicted and put to death without ever seeing any one of his accusers take the stand.”
But Bryan Whitman, a Pentagon spokesman, said the government’s case that Mr. Nashiri was Al Qaeda’s key organizer of the Cole attack was “solid,” and characterized the legal protections available to the defendant as “unprecedented in the history of modern warfare.”
“The fact that many of the potential witnesses are citizens of other nations who cannot be compelled to attend trial in the United States is one of several evidentiary concerns that make trial by military commissions the proper legal venue,” Mr. Whitman said.
The case against Mr. Nashiri also includes some evidence the defense is likely to portray as circumstantial: business records with his name or aliases related to the renting of safe houses and the registration of cars used in the operation, as well as the purchase of the small boat on which two suicide-bombers carried the explosives to the side of the Cole as it was refueling in the harbor next to Aden, Yemen, on Oct. 12, 2000.
But unlike Mr. Mohammed, who has repeatedly admitted planning the Sept. 11 attacks, Mr. Nashiri, who was apparently in Afghanistan at the time of the Cole attack, is expected to strongly deny plotting to bomb the warship. While he admitted taking money from Osama bin Laden to buy the boat in a March 2007 military hearing at Guantánamo, he claimed he intended only to start a fishing business.
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