"If the government's case is built on the similarities between Moussaoui's activities and those of the known hijackers, it must account for the fact that, though he shared their allegiance to Al Qaeda and its leader, Osama bin Laden, his behavior in America was strikingly different from theirs. The government has found evidence of e-mails and meetings among the nineteen, but none between any of them and Moussaoui. The hijackers tried to fit in to American life—drinking in bars, for instance. Moussaoui, while in Oklahoma, remained largely aloof, although he was voluble about his Islamic beliefs. He criticized members of a mosque in Norman for not lowering their gaze when meeting women and for looking at lightly clad cheerleaders. "He went around making a nuisance of himself everywhere he went," Frank W. Dunham, Jr., the federal public defender in charge of Moussaoui's defense team, said. "He was not flying under the radar by any means." Another Moussaoui attorney depicted him as "wearing his fundamentalism on his sleeve," and said, "He was incredibly argumentative—always."

Also of note is the high bar the Justice Department has set for itself in seeking the death penalty against him:

"It accused Moussaoui of a level of involvement that included advance knowledge of the plans, and of the scope and intent of the mission. In this view, he wasn't just a candidate for the twentieth hijacker: he was one of the actual hijackers in all but the final execution, and was prevented from acting on his intentions only by his arrest. "

Yet there is little evidence to support that theory. And still the Justice Department is not seeking any kind of deal with Moussaoui to spare his life in exchange for his information.

The article quotes FBI officials as believing the Justice Department is screwing up the larger terror investigation by going to court in this case where sensitive information will undoubtedly be released.

"The Moussaoui case has also contributed to discontent within the F.B.I. over what some see as a politicized Justice Department more eager to have splashy court victories than to protect intelligence resources. One senior F.B.I. official noted, with obvious disdain, that the Justice Department attorneys wanted to use raw intelligence from sensitive, ongoing investigations to bolster otherwise flagging counterintelligence or counterterrorism criminal cases. "You'd make one case but lose thirty others," the official said. An intelligence official confirmed the dispute, and depicted the Bush Administration as still looking for "the right balance between the prosecution of crime, its prevention, and intelligence."

Hersh concludes with the theory that "Moussaoui was certainly connected to Al Qaeda, but his real value to the United States may have been as a witness and not as a stand-in for the dead hijackers, who are beyond punishment. That potential appears to have been traded away for the sake of a high-profile prosecution that is politically and emotionally satisfying. Moussaoui's arrest, one former C.I.A. official told me, "was totally circumstantial. They cast a wide net and the guy happened to be a little fish who got caught up in it. They know it now. And nobody will back off."