When Sept. 11, 2001, dawned, the Northeast Air Defense Sector in Rome, N.Y., went on full alert — to prepare for a training exercise that envisioned a sneak attack by Russian planes flying over the North Pole to bomb the United States, a prospect that Defense Secretary Robert McNamara had dismissed as outdated in 1966. Later that morning, after American Airlines Flight 11 and United Airlines Flight 175 had hit the World Trade Center and American Airlines Flight 77 the Pentagon, three F-16 fighter jets were scrambled from Langley Air Force Base to form a combat air patrol over Washington. But degraded radio transmission quality meant that the pilots were left clueless about the nature of their mission. On seeing the Pentagon in flames, the lead fighter pilot later explained, “I reverted to the Russian threat. . . . I’m thinking cruise missile threat from the sea. You know, you look down and see the Pentagon burning, and I thought the bastards snuck one by us. . . . You couldn’t see any airplanes, and no one told us anything.”

For all the trillions of dollars lavished on it, for all the talk about confronting new security threats, for all the exhortations to reinvent government, America’s defense establishment, as John Farmer reminds us in “The Ground Truth,” continued to fight the cold war more than a decade after it had ended. Preoccupied with building a costly missile defense system to counter a spurious menace from Russia and with maintaining “full spectrum dominance” over the rest of the globe, most Bush administration officials blithely ignored the danger emanating from the caves of Afghanistan, where Osama bin Laden and his acolytes plotted against America. Confronted by a small group of mostly Saudi nationals armed with box cutters, the central nervous system of the country’s defense agencies went into a state of cataleptic shock. The only decisive action taken on 9/11 came not from the military, but from the courageous passengers who stormed the cockpit of United Airlines Flight 93, leading the hijackers to crash the plane over Pennsylvania farmland before it could reach its intended target in Washington.

As senior counsel to the 9/11 Commission, Farmer, who was the attorney general of New Jersey and is the dean of the Rutgers School of Law, investigated the derelict conduct of the national security apparatus. He was well prepared to do so. In their valuable account of the commission’s activities, “Without Precedent,” the commission chairman, Thomas Kean, and the vice chairman, Lee Hamilton, noted that shortly after the attacks, Farmer — “one of our most important hires” — ­established a victims’ assistance center in New Jersey and helped the F.B.I. uncover important evidence in garbage at Newark International Airport. But the commission’s efforts to reconstruct the tragedy itself were, at best, resented and, at worst, impeded by the sprawling defense bureaucracy and the Bush administration, both of which had much to hide. Even two reports by the inspectors general of the Defense and Transportation Departments, released in 2006, whitewashed government failures. Now that numerous transcripts and tapes have been declassified, however, Farmer draws on them to assail the government’s official depiction of 9/11 as so much public relations flimflam.

Perhaps nothing perturbs Farmer more than the contention that high-ranking officials responded quickly and effectively to the revelation that Qaeda attacks were taking place. Nothing, Farmer indicates, could be further from the truth: President George W. Bush and other officials were mostly irrelevant during the hijackings; instead, it was the ground-level commanders who made operational decisions in an ad hoc fashion. The memoirs of the White House terrorism expert Richard Clarke, which Farmer credits with good faith, make it sound as though a dramatic video­conference that Clarke led played a crucial role in organizing a response to the hijackings, but Farmer says that “this account does not square in any significant respect with what occurred that morning.”