The warnings were going straight to President Bush each morning in his briefings by the CIA director, George Tenet, and in the presidential daily briefings. It would later be revealed by the 9/11 commission into the September 11 attacks that more than 40 presidential briefings presented to Bush from January 2001 through to September 10, 2001, included references to bin Laden. And nearly identical intelligence landed each morning on the desks of about 300 other senior national security officials and members of Congress in the form of the senior executive intelligence brief, a newsletter on intelligence issues also prepared by the CIA.

The senior executive briefings contained much of the same information that was in the presidential briefings but were edited to remove material considered too sensitive for all but the President and his top aides to see. Often the differences between the two documents were minor, with only a sentence or two changed between them. Apart from the commission's chief director, Philip Zelikow, the commission's staff was never granted access to Bush's briefings, except for the notorious August 2001 briefing that warned of the possibility of domestic al-Qaeda strikes involving hijackings. But they could read through the next best thing: the senior executive briefings. During his 2003 investigations it was startling to Mike Hurley, the commission member in charge of investigating intelligence, and the other investigators on his team, just what had gone on in the spring and summer of 2001 - just how often and how aggressively the White House had been warned that something terrible was about to happen. Since nobody outside the Oval Office could know exactly what Tenet had told Bush during his morning intelligence briefings, the presidential and senior briefings were Tenet's best defence to any claim that the CIA had not kept Bush and the rest of the Government well-informed about the threats. They offered a strong defence. The team's investigators began to match up the information in the senior briefings and they pulled together a timeline of the headlines just from the senior briefings in the northern spring and summer:

"Bin Ladin Planning Multiple Operations" (April 20)and "Bin Ladin Threats Are Real" (June 30)It was especially troubling for Hurley's team to realise how many of the warnings were directed to the desk of one person: Condoleezza Rice, the National Security Adviser. Emails from the National Security Council's counter-terrorism director, Richard Clarke, showed that he had bombarded Rice with messages about terrorist threats. He was trying to get her to focus on the intelligence she should have been reading each morning in the presidential and senior briefings "Bin Ladin Public Profile May Presage Attack" (May 3)

"Terrorist Groups Said Co-operating on US Hostage Plot" (May 23) "Bin Ladin's Networks' Plans Advancing" (May 26) "Bin Ladin Attacks May Be Imminent"

(June 23) "Bin Ladin and Associates Making Near-Term Threats" (June 25)

"Bin Ladin Planning High-Profile Attacks" (June 30), "Planning for Bin Ladin Attacks Continues, Despite Delays" (July 2)

Other parts of the Government did respond aggressively and appropriately to the threats, including the Pentagon and the State Department. On June 21, the US Central Command, which controls American military forces in the Persian Gulf, went to "delta" alert - its highest level - for American troops in six countries in the region. The American embassy in Yemen was closed for part of the summer; other embassies in the Middle East closed for shorter periods. But what had Rice done at the NSC? If the NSC files were complete, the commission's historian Warren Bass and the others could see, she had asked Clarke to conduct inter- agency meetings at the White House with domestic agencies, including the Federal Aviation Administration and the FBI, to keep them alert to the possibility of a domestic terrorist strike.

She had not attended the meetings herself. She had asked that the then attorney-general, John Ashcroft, receive a special briefing at the Justice Department about al-Qaeda threats. But she did not talk with Ashcroft herself in any sort of detail about the intelligence. Nor did she have any conversations of significance on the issue with the FBI director, Louis Freeh, nor with his temporary successor that summer, the acting director Tom Pickard. There is no record to show that Rice made any special effort to discuss terrorist threats with Bush. The record suggested, instead, that it was not a matter of special interest to either of them that summer. Bush seemed to acknowledge as much in an interview with Bob Woodward of The Washington Post that Bush almost certainly regretted later. In the interview in December 2001, only three months after the attacks, Bush said that "there was a significant difference in my attitude after September 11" about al-Qaeda and the threat it posed to the United States.

Before the attacks, he said: "I was not on point, but I knew he was a menace, and I knew he was a problem. I knew he was responsible, or we felt he was responsible, for the previous bombings that killed Americans. I was prepared to look at a plan that would be a thoughtful plan that would bring him to justice, and would have given the order to do that. I have no hesitancy about going after him. But I didn't feel that sense of urgency, and my blood was not nearly as boiling." If anyone on the White House staff had responsibility for making Bush's blood "boil" that summer about Osama bin Laden, it was Rice.

The members of Mike Hurley's team were also alarmed by the revelations, week by week, month by month, of how close the commission's chief director, Philip Zelikow, was to Rice and others at the White House. They learned early on about Zelikow's work on the Bush transition team in 2000 and early 2001 and about how much antipathy there was between him and Richard Clarke. They They heard the stories about Zelikow's role in developing the "pre-emptive war" strategy at the White House in 2002. Zelikow's friendships with Rice and others were a particular problem for Warren Bass, since Rice and Clarke were at the heart of his part of the investigation. It was clear to some members of team that they could not have an open discussion in front of Zelikow about Rice and her performance as National Security Adviser. They could not say openly, certainly not to Zelikow's face, what many on the staff came to believe: that Rice's performance in the spring and summer of 2001 amounted to incompetence, or something not far from it. David Kay, the veteran American weapons inspector sent to Iraq by the Bush Administration in 2003 to search for weapons of mass destruction, passed word to the commission that he believed Rice was the "worst national security adviser" in the history of the job.

For Hurley's team, there was a reverse problem with Clarke. It was easy to talk about Clarke in Zelikow's presence, as long as the conversation centred on Clarke's failings at the NSC and his purported dishonesty. Long before Bass had seen Clarke's files, Zelikow made it clear to the team's investigators that Clarke should not be believed, that his testimony would be suspect.

He argued that Clarke was a braggart who would try to rewrite history to justify his errors and slander his enemies, Rice in particular. The commission had decided that in its private interviews with current and former government officials, witnesses would be placed under oath when there was a substantial reason to doubt their truthfulness. Zelikow argued that Clarke easily fell into that category; Clarke, he decreed, would need to be sworn in. When he finally got his security clearance and was allowed into the reading room, Bass discovered he could make quick work of Rice's emails and internal memos on the al-Qaeda threat in the spring and summer of 2001. That was because there was almost nothing to read, at least nothing that Rice had written herself. Either she committed nothing to paper or email on the subject, which was possible since so much of her work was conducted face-to-face with Bush, or terrorist threats were simply not an issue that had interested her before September 11. Her speeches and public appearances in the months before the attacks suggested the latter.

Tipped off by an article in The Washington Post, the commission discovered the text of a speech that she had been scheduled to make on September 11, 2001 - the speech was canceled in the chaos following the attacks - in which Rice planned to address "the threats of today and the day after, not the world of yesterday". The speech, which was intended to outline her broad vision on national security and to promote the Bush Administration's plans for a missile defence system, included only a passing reference to terrorism and the threat of radical Islam. On the day that Osama bin Laden launched the most devastating attack on the United States since Pearl Harbour, bin Laden's terrorist network was seen by Rice as only a secondary threat, barely worth mentioning. But if Rice had left almost no paper trail on terrorism in 2001, Clarke's files were everything that Bass could have hoped for. Clarke wrote down much of what he saw and heard at the White House, almost to the point of obsession when it came to al-Qaeda. Bass and his colleagues could see that Clarke had left a rich narrative of what had gone so wrong at the NSC in the months before September 11, albeit filtered through the writings of the very opinionated Clarke.

Repeatedly in 2001, Clarke had gone to Rice and others in the White House and pressed them to move, urgently, to respond to a flood of warnings about an upcoming and catastrophic terrorist attack by Osama bin Laden. The threat, Clarke was arguing, was as dire as anything that he or the CIA had ever seen. He pushed for an early meeting in 2001 with Bush to brief him about bin Laden's network and the "nearly existential" threat it represented to the United States. But Rice rebuffed Clarke. She allowed him to give a briefing to Bush on the issue of cyber terrorism, but not on bin Laden; she told Clarke the al-Qaeda briefing could wait until after the White House had put the finishing touches that summer on a broader campaign against bin Laden. She moved Clarke and his issues off centre stage - in part at the urging of Zelikow and the transition team. Bass told colleagues that he gasped when he found a memo written by Clarke to Rice on September 4, 2001, exactly a week before the attacks, in which Clarke seemed to predict what was just about to happen. It was a memo that seemed to spill out all of Clarke's frustration about how slowly the Bush White House had responded to the cascade of terrorist threats that summer. The note was terrifying in its prescience.

"Are we serious about dealing with the al-Qaeda threat?" he asked Rice. "Decision makers should imagine themselves on a future day when the CSG [Counterterrorism Security Group] has not succeeded in stopping al-Qaeda attacks and hundreds of Americans lay dead in several countries, including the US. Bass's colleagues said he knew instantly that the September 4 email was so sensitive - and potentially damaging, especially to Rice - that the White House would never voluntarily release a copy to the commission or allow him to take notes from the room if they came close to reproducing its language. Under a written agreement between the commission and the White House, notes could not "significantly reproduce" the wording of a classified document.

Bass decided he would have to try to memorise it in pieces, several sentences at a time, and then rush back to the commission to bat them out on a computer keyboard. The day he discovered the document, Bass all but burst into the commission's offices and rushed over to Hurley. "Holy shit, chief," Bass said excitedly. "You won't believe what I found."

He told Hurley that Clarke's September 4 memo was a "document that grabs you by the throat, a document that you write when you're at the end of your tether - or well past it", as Clarke clearly was in the weeks before September 11. Hurley instantly understood the significance of what he was being told by Bass. The question for both men was whether Zelikow would allow them to share any of it with the public. Months later, Bass could not take it any longer. He was going to quit, or least threaten to quit, and he was going to make it clear that Zelikow's attempts at interference - his efforts to defend Rice and demean Clarke - were part of the reason why. He marched into the office of Dan Marcus, the general counsel, to announce his threat to leave the investigation.

"I cannot do this," he declared to Marcus, who was already well aware of Bass's unhappiness. "Zelikow is making me crazy." He was outraged by Zelikow and the White House; Bass felt the White House was trying to sabotage his work by its efforts to limit his ability to see certain documents from the NSC files and take useful notes from them. Marcus urged him to calm down: "Let's talk this through." But Bass made it clear to colleagues that he believed Zelikow was interfering in his work for reasons that were overtly political - intended to shield the White House, and Rice in particular, from the commission's criticism. For every bit of evidence gathered by Bass and Hurley's team to bolster Clarke's allegation that the White House had ignored terrorist threats in 2001, Zelikow would find some reason to disparage it. Marcus and Hurley managed to talk Bass out of resigning, although the threat lingered until the final weeks of the investigation.

On May 15, 2002, CBS network reported that a daily briefing presented to Bush a few weeks before the September 11 attacks warned him specifically about the threats of a domestic hijacking by al-Qaeda. Instead of releasing the briefing or at least offering a detailed explanation of what was in the document, the White House chose to have Rice hold a news conference at the White House in which she raised as many questions about the briefing as she answered.

It would later become clear to many of the commission's members and its staff that she had tried to mislead the White House press corps about the contents of the briefing. She acknowledged that Bush had received a briefing about possible al-Qaeda hijackings, but she claimed that the brief offered "historical information" and "was not a warning - there was no specific time, place, or method". She failed to mention, as would later be clear, that the briefing focused entirely on the possibility that al-Qaeda intended to strike within the United States; it cited relatively recent FBI reports of possible terrorist surveillance of government buildings in New York.

Tom Kean, the commission's chairman, could not deny the thrill of this. A former governor of New Jersey who had left politics to become president of Drew University in his home state, Kean took a seat in the reading room in the New Executive Office building where the commission was reviewing the White House's most secret files. Kean was handed a sheaf of presidential briefings from the Clinton and Bush administrations. Here in his hands were the documents that the White House had been so determined for so long to keep from him. Lee Hamilton liked to refer to the briefings as the "holy of holies" - the ultimate secret documents in the government - and Kean assumed that must be the case.

"I thought this would be the definitive secrets about al-Qaeda, about terrorist networks and all the other things that the President should act on," he said. "I was going to find out the most important things that a president had learned." He assumed they would contain "incredibly secretive, precise, and accurate information about anything under the sun." Each brief was only several pages long, so Kean could read through months of them in a stretch of a few hours. And he found himself terrified by what he was reading, really terrified. Here were the digests of the most important secrets that were gathered by the CIA and the nation's other spy agencies at a cost of tens of billions of dollars a year.

And there was almost nothing in them. "They were garbage," Kean said. "There really was nothing there - nothing, nothing."

If students back at Drew turned in term papers this badly researched, "I would have given them an F," he said. Kean pointed that out to one of his White House minders who accompanied him to the reading room. "I've read all this," he told the minder in astonishment. A lot of the information in the briefings and other supposedly top secret intelligence reports had already been revealed by the nation's big news organisations. "I already knew this." "Oh, but you're missing the point," the minder replied. "Now you know it's true." It occurred to Kean that this might be the commission's most frightening discovery of all: The emperors of espionage had no clothes. Perhaps the reason the White House had fought so hard to block the commission's access to the briefings was that they revealed how ignorant the Government was of the threats it faced before September 11. Kean could understand their fear. Imagine the consequences if al-Qaeda and its terrorist allies knew how little the US really knew about them.

Commission member Jamie Gorelick, who, along with Zelikow, was given access to the larger universe of briefings, was more impressed by the documents than Kean had been. Or at least she was less unimpressed. She knew the Bush Administration was right to complain that much of the intelligence in the briefs in the months before September 11 was maddeningly non-specific about a possible date or place of an attack. Some of the intelligence in the briefs was "paltry"; sometimes the information contradicted itself from one day to the next, Gorelick said. But she was astonished by the sheer volume of the warnings. Flood, cascade, tsunami, take your pick of metaphors. She could see that in the spring and summer of 2001, there was a consistent drum beat of warnings, day after day, that al-Qaeda was about to attack the United States or its allies. It was clear to Gorelick that the CIA had gone to Bush virtually every morning for months in 2001 to give him the message that the United States needed to be ready for a catastrophic terrorist strike, and from what she was reading, no one ruled out the possibility of a domestic attack.

"Something is being planned, something spectacular," she said, summarising what the President had been told by George Tenet and what Bush should have read in the briefings. "We don't know what it is, we don't know where it is, but something is happening." She said CIA analysts were trying to tell Bush, as bluntly as they could, that the threat in those months was "the worst thing they've ever seen - an unprecedented threat," worse than the threats before the millennium. It seemed to Gorelick that Rice had "assumed away the hardest part of her job" as national security adviser - gathering the best intelligence available to the White House and helping the President decide how to respond to it. Whatever her job title, Rice seemed uninterested in actually advising him. Instead, she wanted to be his closest confidant - specifically on foreign policy - and to simply translate his words into action. Rice had wanted to be "the consigliere to the President", Gorelick thought.

Domestic issues seemed to bore her. Her deputy, Stephen Hadley, had told the commission something remarkable in his private interview the month before: He and Rice had not seen themselves as responsible for co-ordinating the FBI and other domestic agencies about terrorism. But if they weren't responsible, who was? There was no separate domestic security adviser in the White House. They had just demoted Clarke. At the time of her May 2002 news conference, no reporter had a copy of the presidential briefing. CBS had broken the story of its existence but had few details of what was actually in the document. So the White House press corps would have to trust Rice's description of what was in it.

She described it as a "warning briefing but an analytic report" about al-Qaeda threats and said that it contained "the most generalised kind of information - there was no time, there was no place, there was no method of attack" mentioned apart from a "very vague" concern about hijacking. "I want to reiterate," she said. "It was not a warning." Asked if September 11 didn't represent an intelligence failure by the Administration, she replied almost testily: "I don't think anybody could have predicted that these people would take an airplane and slam it into the World Trade Centre, take another one and slam it into the Pentagon - that they would try to use an airplane as a missile." Rice's news conference came eight months after the attacks. Yet she was suggesting that in all that time, no one had bothered to tell her that there were indeed several reports prepared within the CIA, the aviation administration, and elsewhere in the Government about the threat of planes as missiles.

Had no one told her in all those months that the Department of Defence had conducted drills for the possibility of a plane-as-missile attack on the Pentagon? Had she forgotten that when she and Bush attended the G8 summit in Italy in July 2001, the airspace was closed because of the threat of an aerial suicide attack by al-Qaeda? Commission member Tim Roemer made it his goal to get the August 6 briefing made public and to prove once and for all that Rice and her White House colleagues had a concept of the truth about September 11 that was, at best, "flexible". To Roemer, Rice had long ago passed the "threshold" between spin and dishonesty.

"She'd lost credibility with me," he said. The question among the Democratic commissioners was whether anybody would be brave enough to go public to question Rice's competence and her honesty. Much as the staff felt beaten down by Zelikow, so did the other Democratic commissioners. By the end, they had given up the fight to document the more serious failures of Bush, Rice, and others in the Administration in the months before September. Zelikow would never have permitted it. Nor, they realised, would Kean and Hamilton. The Democrats hoped the public would read through the report and understand that September 11 did not have to happen - that if the Bush Administration had been more aggressive in dealing with the threats flooding into the White House from January 2001 through to September 10, 2001, the plot could have been foiled. The Clinton administration could not duck blame for having failed to stop bin Laden before 2001. But what had happened in the White House in the first eight months of George Bush's presidency had all but guaranteed that 19 young Arab men with little more than pocket knives, a few cans of mace, and a misunderstanding of the tenets of Islam could bring the US to its knees.

The Commission - The Uncensored History Of The 9/11 Investigation by Philip Shenon (Little, Brown, $35) is published on Monday.