The death of Dr David Kelly and the events that led to it are a triple tragedy. They are a tragedy for his family, a tragedy for the better scrutiny of government and a tragedy for investigative journalism. Lord Hutton has pronounced, magisterially and disdainfully, peering from on high at the sordid and frantic events that culminated in the suicide of a scientist who, in the judge's own words, served his country with great distinction and then slit his wrists in an Oxfordshire ditch. Hutton's report is, unlike intelligence assessments and more like the infamous September dossier at the centre of the dispute, shockingly shorn of qualification or calibration. In essence, the judge has said that the BBC was absolutely wrong and that Tony Blair, his aides and his ministers, apart from the odd glitch here and there, were essentially right to confront the corporation in the way they did. After all these years of battling with the media, Blair and Alastair Campbell can now scarcely contain their glee. Gotcha!

For Blair, after escaping in the vote on top-up fees thanks to the intervention of Gordon Brown, the events of the past week ended far better than he had dared hope. He will now declare that it is time to draw a line, to move on and focus on the domestic agenda, to capitalise on the moment to prepare for the general election.

He will declare the controversy about the war over. In that, he will be wrong. On another point, however, the Prime Minister is correct. "It is absolutely right that people can question whether the intelligence received was right; and why we have not yet found weapons of mass destruction," Blair told the Commons, minutes after Hutton had delivered his verdict. "There is an entirely legitimate argument about the wisdom of the conflict. I happen to believe now, as I did in March, that removing Saddam Hussein has made the world a safer and better place. But others are entirely entitled to disagree. However, all of this is of a completely different order from a charge of deception, of duplicity, of deceit, a charge that I or anyone else deliberately falsified intelligence."

These, as Blair rightly asserts, are accusations of a different level. The tragedy of Andrew Gilligan is that he conflated the two, with his apparent "slip of the tongue" that intelligence had been inserted into the dossier, notably the 45-minute claim, by people in Downing Street who "knew it was wrong". They hoped it was right. They did not know it was right. But what evidence did he produce to prove that they knew it to be wrong?

The parameters for the charge against the government are narrower, but no less significant. In my book Blair's Wars, I investigated the circumstances that led Blair to take Britain to war five times in six years. I found that Blair had committed himself to joining George W Bush in a conflict against Iraq, come what may, back in April 2002. From that point, he was locked in. He sought intelligence to help make the case for him, knowing that he would have trouble persuading his party, or his Attorney-General, on the basis of regime change. Intelligence was there. It did not have to be made up, but it did have to be "presented". Intelligence is hedged, often contradictory, and - a point frequently lost - often more an intellectual than empirical exercise. It is often a question of judgement rather than fact.

Blair likes to claim that all countries believed in the intelligence. What he deliberately does not say is that they assessed that intelligence in different ways. As one European official put it to me at the time: "Out of the same grapes in a vineyard you can make a very different wine." One could have used exactly the same intelligence to make the case for a) immediate war, b) a delay pending further inquiries by Hans Blix, or c) no war.

The absence of proof that Saddam had destroyed each and every biological and chemical substance he had been known to have before the first Gulf war of 1991 was interpreted by the UK and the US - but by almost no one else - as confirmation that he still had it. The spooks had made that lazy assumption long before Blair asked them to help with his dossier. Similarly Gilligan made two lazy assumptions: that, because the dossier was - even by Campbell's own admission - "strengthened in places", it was by definition all made up; and that, because several intelligence officials lower down the food chain (we all spoke to them) had their reservations, the spy chiefs had been steamrollered by No 10. Anyone who was rigorously following the issue at the time knew that they were all in it together.

In the United States, the evidence was mounting of a bigger conspiracy. A recent report from the Carnegie Endowment for International Peace concludes: "Administration officials systematically misrepresented the threat from Iraq's WMD and ballistic missile programmes." Still, one didn't need to accuse the government of lying - and I didn't - to assert the case that we may have been taken to war on a false pretext.

Hutton himself declares, struggling to restrain his contempt for the fourth estate: "The term 'sexed up' is a slang expression, the meaning of which lacks clarity in the context of the discussion of the dossier." He dismisses out of hand the suggestion that it was "embellished with items of intelligence known or believed to be false or unreliable". But he says it could be interpreted as being "drafted in such a way as to make the case against Saddam Hussein as strong as the intelligence contained in it permitted". In those terms, "it could be said that the government 'sexed up' the dossier".

The initial reaction among MPs and others who have been probing the government on Iraq ranged from "whitewash" to "blinkered". Hutton's lasting contribution to the debate is likely to confirm the convictions of those who believe Blair and Bush did the decent thing and that all other factors are irrelevant, and to confirm the convictions of those who believe they were duped on the road to war.

Where was any reference in the report to Campbell's diaries, not so much for his fruity language, but for the light they shed on his relationship with John Scarlett, the chairman of the Joint Intelligence Committee? Where was any reference to the copious material submitted to the inquiry, and chewed over at length, to the drafting process of the dossier? Where was any reference to e-mails from the likes of Jonathan Powell, Blair's chief of staff, expressing concern that the dossier would not convince anyone who did not already believe Saddam was dangerous? Where was the admission by another senior No 10 official at the time, Philip Bassett, that he thought "we're in a lot of trouble as it stands now"? Where is any reference to the effect the changes in wording had on public perceptions of the immediacy of the threat posed by Saddam? Where is any reference to the Chinese walls that had long existed between the JIC and No 10? Several senior intelligence and diplomatic figures have expressed concern at the extent of the matey-ness between Campbell and Scarlett.

The best that Hutton offered on that score was the following: "I consider that the possibility cannot be completely ruled out that the desire of the Prime Minister to have a dossier which, whilst consistent with the available intelligence, was as strong as possible in relation to the threat posed by Saddam Hussein's WMDs, may have subconsciously influenced Scarlett and other members of the JIC to make the wording of the dossier somewhat stronger than it would have been if it had been contained in a normal JIC assessment." Even on this point he draws back, going on to say he was confident that Scarlett and the others would have been "concerned to ensure that the contents of the dossier were consistent with the intelligence available to the JIC".

The list of omissions by Hutton is as compelling as the list of conclusions. Where was any reference to the so-called "dodgy dossier" of January 2003 that brought the whole process into disrepute? And where was any reference, by way of setting out the context, for intelligence assertions that turned out - well before the war - to be categorically false, such as the British claim echoed by George W Bush that Iraq had sought to buy uranium from Niger?

Whenever Hutton was asked to confront a difficult issue, he seemed to suggest it was outside his remit. Not only did he say he was not charged with casting judgement on the biggest question of all - the disappearing trick of the WMDs - but he divested himself of the responsibility to look into other issues, such as the refusal of the government to correct the false impression that the chemical threat related to long-range missiles rather than battlefield shells.

This report is even more naIve than Sir Richard Scott's findings on that other sorry tale of British dealings with Iraq. Back in 1996, a judge gave John Major's government a lifeline by weaving caveats into each and every line of criticism of illegal arms sales to Saddam's regime. This time, Hutton made no such tactical errors. He sought to ensure that he and he alone interpreted his report, delaying its publication until after he had spoken. He tried, and failed, to prevent any leaks, but this was no war of spin. His conclusions were unequivocal.

And yet he failed to see that, by declaring unreservedly in favour of the government and against the BBC, he would give Blair carte blanche to declare Iraq done with. He has made the process of uncovering the bigger truths all the harder. When and how will Blair account for the many twists and turns on the road to war, shifting his rationale to suit the moment. When and how will Blair come clean on WMDs? Perhaps now he never will. "Our best hope is that the public will see this as so ludicrously blinkered, people will dismiss this report out of hand," said one MP. Certainly the absurd faux indignation of Michael Howard and the Conservative one-time cheerleaders for war does not help the process.

The events of the past six months are a tragedy for journalism, and for a particular nascent type of BBC journalism. The corporation was beginning to break out of its "on the one hand, on the other, only time will tell" straitjacket that had dictated coverage for decades. It was beginning to ask searching questions, to allow its senior correspondents to go out on a limb, to "call" stories and to get stories.

Gilligan was on to something, as many other journalists were at the time. He was investigating concerns that corners had been cut in the use of intelligence to make the case for war. As Blair correctly pointed out, the September dossier wasn't such a big deal at the time. Nor was it really challenged at the time (another example of lazy journalism). But it did come into play more and more, the closer we came to conflict.

Kelly did not give Gilligan a story, one with specific facts. He did give him a steer. He did help him to paint a picture. But that was all. Gilligan's tragedy was to sex up what he had been told, in so doing undermining the case against the government. By last summer, many around Blair were growing increasingly agitated by the failure to find WMDs, about accounting for what they had said and done on the road to war. Campbell went for Gilligan partly because he was angry with him, but also partly because he knew he could get him.

The woeful lack of supervision and the sloppy processes of investigation by BBC managers only compounded the problem. As the corporation embarks on the long haul back to respectability, those few within its ranks who believe in investigative journalism are wondering what the future holds. Ask yourself, the next time the government gets in a scrape, will the BBC be out there breaking the story, or hiding meekly behind the revelations of others?

A few weeks ago, amid all the speculation about the date of the report, one of the explanations doing the rounds was that Hutton was worried about the powers at his disposal to bring down the government. How absurd that all feels now. It was not that Hutton feared causing Blair sleepless nights. He simply believed that there was no case to answer. A grubby journalist had impugned the Prime Minister's integrity. The Prime Minister had not lied, and that was that.

Blair has got out of jail free, courtesy of a judge who in the best traditions of the British establishment strained every sinew to give the government the benefit of the doubt. Whatever Scott could do, Hutton has done better.