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When hundreds of prisoners arrived at the American naval base in Guantánamo Bay, Cuba, in early 2002, the Bush administration laid out a straightforward plan: once the men were interrogated, the worst of the lot would be prosecuted before special military tribunals devised to bring terrorists to justice quickly. A year later, with no trials yet in sight, some officials at the highest levels of the Bush administration began privately venting their frustration about both the slow pace of the Pentagon's new courts and the soundness of their rules. Attorney General John Ashcroft was especially vocal. "Timothy McVeigh was one of the worst killers in U.S. history," Mr. Ashcroft said at one meeting of senior officials, according to two of those present. "But at least we had fair procedures for him." The administration invoked extraordinary wartime powers to set up the new system of military justice, arguing that the Sept. 11 attacks and the continuing threat they exposed justified the use of legal authorities that had not been exercised since World War II. But as officials sought to apply those powers to a very different kind of conflict, they became mired in problems they are still struggling to solve. Although White House lawyers said they rushed to devise a new judicial structure that could handle serious Qaeda terrorists, many of the detainees sent to Guantánamo turned out to be low-level militants, Taliban fighters and men simply caught in the wrong place at the wrong time. [more

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