In the summer of 2003, Warren Bass, an investigator for the 9/11 Commission, was digging through highly classified National Security Council documents when he came across a trove of material that startled him. Buried in the files of former White House counterterrorism czar Richard Clarke, the documents seemed to confirm charges that the Bush White House had ignored repeated warnings about the threat posed by Osama bin Laden. Clarke, it turned out, had bombarded national-security adviser Condoleezza Rice in the summer of 2001 with impassioned e-mails and memos warning of an Al Qaeda attack—and urging a more forceful U.S. government response. One e-mail jumped out: it pleaded with officials to imagine how they would feel after a tragedy where "hundreds of Americans lay dead in several countries, including the U.S.," adding that "that future day could happen at any time." The memo was written on Tuesday, Sept. 4, 2001—just one week before the attacks on New York's World Trade Center and the Pentagon.

But when Bass tried to impress the significance of what he had discovered upon the panel, he ran into what he thought was a roadblock—his boss. Philip Zelikow, a respected University of Virginia historian hired to be the 9/11 Commission's executive director, had long been friendly with Rice. The two had coauthored a book. Rice had later placed him on a Bush transition team that reorganized the NSC (and ended up diminishing Clarke's role). At Rice's request, Zelikow had also anonymously drafted a new Bush national-security paper in September 2002 that laid out the case for preventive war.

In commission staff meetings, Zelikow disparaged Clarke as an egomaniac and braggart who was unjustly slandering his friend Rice, according to a new book, "The Commission: The Uncensored History of the 9/11 Investigation," by New York Times reporter Philip Shenon. Bass was so disturbed by what he saw as Zelikow's bullying that at one point he threatened to resign. So did a Democratic commissioner, Bob Kerrey, when he discovered Zelikow's ties to the administration. "Look, Tom, either he goes or I go," Kerrey told the panel's chairman, Republican Tom Kean, about Zelikow, according to Shenon....

In any case, the suggestion by conspiracy theorists—who have seized on the evidence in Shenon's book—that Zelikow was serving as a secret White House"mole" is hard to sustain. As some of the 9/11 commissioners themselves pointed out, Zelikow—despite his occasionally abrasive style—oversaw the production of a hard-hitting report that disclosed an unprecedented amount of previously secret information....