America was under attack, and somebody had to make a decision. Dick Cheney, huddled in the Presidential Emergency Operations Center under the White House, had just urged the traveling George W. Bush not to return to Washington. The president had left Florida aboard Air Force One at 9:55 a.m. on 9/11 "with no destination at take-off," as last week's 9-11 Commission report noted. Nor had Bush given any known instructions on how to respond to the attacks. Now Cheney faced another huge decision on a morning in which every minute seemed monumental. The two airliners had already crashed into the Twin Towers, another into the Pentagon. Combat air patrols were aloft, and a military aide was asking for shoot-down authority, telling Cheney that a fourth plane was "80 miles out" from Washington. Cheney didn't flinch, the report said. "In about the time it takes a batter to decide to swing," he gave the order to shoot it down, telling others the president had "signed off on the concept" during a brief phone chat. When the plane was 60 miles out, Cheney was again informed and again he ordered: take it out.

Then Joshua Bolten, after what he described in testimony as "a quiet moment," spoke up. Bolten, the White House deputy chief of staff, asked the veep to get back in touch with the president to "confirm the engage order." Bolten was clearly subordinate to Cheney, but "he had not heard any prior conversation on the subject with the president," the 9/11 report notes. Nor did the real-time notes taken by two others in the room, Cheney's chief of staff, "Scooter" Libby--who is known for his meticulous record-keeping--or Cheney's wife, Lynne, reflect that such a phone call between Bush and Cheney occurred or that such a major decision as shooting down a U.S. airliner was discussed. Bush and Cheney later testified the president gave the order. And national-security adviser Condoleezza Rice and a military aide said they remembered a call, but gave few specifics. The report concluded "there is no documentary evidence for this call."

Did Dick Cheney follow proper procedures in ordering the shoot-down of U.S. airliners on 9/11? Well, almost no one seemed to follow procedures that day simply because there were none, the 9-11 Commission concludes. NORAD (the U.S. air defense command), the Federal Aviation Administration and air-traffic controllers faced "an unprecedented challenge they had never encountered and had never trained to meet." The issue was moot anyway: by the time Cheney issued his shoot-down order, between 10:10 and 10:15 a.m., United Flight 93, the last plane-turned-missile on 9/11, had already crashed in Pennsylvania (at 10:03 a.m.) after its passengers had made their heroic stand. The White House team just didn't know it. And many of the scrambled fighters didn't even have weapons onboard.

But the question of Cheney's behavior that day is one of many new issues raised in the remarkably detailed, chilling account laid out in dramatic presentations by the 9-11 Commission. NEWSWEEK has learned that some on the commission staff were, in fact, highly skeptical of the vice president's account and made their views clearer in an earlier draft of their staff report. According to one knowledgeable source, some staffers "flat out didn't believe the call ever took place." When the early draft conveying that skepticism was circulated to the administration, it provoked an angry reaction. In a letter from White House lawyers last Tuesday and a series of phone calls, the White House vigorously lobbied the commission to change the language in its report. "We didn't think it was written in a way that clearly reflected the accounting the president and vice president had given to the commission," White House spokesman Dan Bartlett told NEWSWEEK. Ultimately the chairman and vice chair of the commission, former New Jersey governor Thomas Kean and former representative Lee Hamilton--both of whom have sought mightily to appear nonpartisan--agreed to remove some of the offending language. The report "was watered down," groused one staffer.

That was a battle lost, but the 9-11 Commission may find that it still wins the war--by writing the history. Two years ago, when the commission was created after emotional lobbying by 9/11 victims' families, the White House didn't take the probe terribly seriously. The administration initially ignored its requests for some key documents, snubbed efforts to get Bush and others to testify and shrugged off threats of subpoenas. But the commission persevered, stoked by the passion of the victims' families, and persuaded the administration to cave on most issues. The skirmishing continues--and it's starting to get personal. Now, with a final report due next month, the Bush team is increasingly aware that the commission's body of work might someday stand as the nation's official record of 9/11. And Bush's credibility on key national-security issues--upon which he's staked his re-election bid--could well turn on whether the public believes the administration's version or the commission's.

This week the 9-11 commissioners find themselves engaged in another testy dispute, especially with Cheney, over the ties between Saddam Hussein and Osama bin Laden. For the Bush team, making the case that Saddam and bin Laden were linked is one of its most sensitive credibility issues, a key justification for following its assault on Al Qaeda with a much costlier and bloodier war in Iraq. The vice president insisted in short-tempered public remarks last week that the commission had agreed the Iraq-Qaeda links were extensive. But commission vice chair Hamilton acknowledged to NEWSWEEK the commissioners had differences with the administration. "We didn't have any evidence of collaboration or cooperation," Hamilton said flatly. He added that bin Laden's ties "to Iran and Pakistan were certainly stronger than any tie he had to Iraq." Despite Cheney's comments, Bartlett said the White House did not officially raise any questions about the report's conclusions on Qaeda-Iraq ties.

Cheney has now challenged the commission point blank. Asked in a CNBC interview whether he had more information about Iraq-Qaeda links than the commission, Cheney remarked, "Probably." This comment stunned Kean and Hamilton, who asked Cheney to pass that extra intel on to them. (Administration spokesmen had previously said they gave the commission whatever it needed to do its job.) The vice president also reasserted his belief that a long-alleged meeting between 9/11 hijacker Muhammad Atta and an Iraqi intel agent on April 9, 2001, in Prague might have occurred. Some 9/11 staffers said they were astonished by this: their report, citing cell-phone records, concludes unambiguously that Atta could not have been in Prague on that date; he was in Florida. (NEWSWEEK has also learned that Czech investigators and U.S. intelligence have obtained corroborated evidence which they believe shows that the Iraqi spy who allegedly met Atta was away from Prague on that day.)

On several occasions since 9/11, in speeches before the Iraq war and since, Cheney has run ahead of Bush on policy, only to be lassoed back in by the White House. In August 2002, he dismissed U.N. inspections just before Bush called for them in a speech. Later that fall the veep suggested in another speech that Iraq might have had a hand in 9/11, forcing Bush to deny later that it did. And some staffers thought it was interesting that Bush and Cheney insisted on testifying before the commission together. (Sources say much of their testimony focused on the shoot-down issue.) So far the two are staying on message in asserting Qaeda-Iraq links.

Ultimately, the clash of views between the White House and the commission could help shape the final 9/11 report--which Kean has insisted is as much about the future as the past. The hard work of trying to prevent another attack is well underway. U.S. officials say that new emergency procedures have vastly improved communications between top policymakers, air-traffic controllers and U.S. military commanders (still, a communications breakdown prompted a panicked evacuation of the Capitol when a plane ventured into restricted airspace during the Reagan funeral). "When it comes to shooting down an aircraft," NORAD commander Gen. Ralph Eberhart told NEWSWEEK, "there are very specific rules of engagement." Presumably the president, vice president and 9-11 Commission will agree on what those should be. And who will make the final call.