So who stands to gain from the smearing of Dr Kelly?

If the scientist was unreliable, it lets both the BBC and ministers off the hook. By Jo Dillon

It all comes down to who said what to whom. But Dr David Kelly, the key witness, is dead. And so the inquiry, sparked by his apparent suicide, will rest on his reputation.

The Government and its most senior figures - Tony Blair, his spin-doctor Alastair Campbell and Defence Secretary Geoff Hoon - have much to lose if the version of events put forward by BBC defence correspondent Andrew Gilligan in his contentious Today programme broadcast, claiming No 10 had "sexed up" the Iraq weapons dossier, proves to be a fair and accurate report of his conversation with Dr Kelly.

It seemed last week that rather than engage with the veracity of the claims, the Government had opted to blacken Dr Kelly's name.

Tom Kelly, the Prime Minister's official spokesman, has already been forced to apologise for branding Dr Kelly a "Walter Mitty" figure, a fantasist who either was not straight with his employers about the nature and scope of his links with journalists or, if that failed to wash, had exaggerated the levels of his knowledge.

Mr Kelly, who clearly acted outside the Prime Minister's official demand for respect and restraint and his insistence that the inquiry led by Lord Hutton and Dr Kelly's funeral should be allowed to proceed unaccompanied by noises off, is adamant this was an "unauthorised" briefing.

When No 10 finally confessed the briefing had taken place, Mr Kelly insisted he had been quoted out of context. He was merely, it has been said, "mulling over possibilities" or the "menu of options" when he made his remarks. Mr Kelly said of his off-the-record briefing: "We were discussing questions, not answers."

That he is understood to have given similar briefings to at least three journalists on the same day and that he spoke to each in his capacity as official spokesman has prompted critics to question whether this was not the Government's official line.

Paul Waugh, The Independent's deputy political editor who broke the "Walter Mitty" story, was every bit as adamant as Mr Kelly in the defence of his report. "His remarks to me were presented as a chronological version of events from Downing Street's point of view," he made clear. He stressed that the remarks made to him, in response to a direct question, were a "narrative sequence". It appears as though Mr Kelly was reading from a prepared briefing paper rather than making a series of off-the-cuff remarks.

Though lobby correspondents are not always each others' natural allies, many at Westminster now believe that Mr Kelly's briefing was a deliberate attempt to "set the tone" for coverage of the Hutton inquiry, that it had always been the Government's intention to question Dr Kelly's reliability and that the briefing would drive home their point by "pouring poison into the ears of the trusted few" correspondents.

In the days that followed, the Deputy Prime Minister, John Prescott, who is understood to be "furious" with Mr Kelly and considers him to have "behaved disgracefully", sought to recover the Government's position. He was assisted in doing so by the sober dignity of Dr Kelly's funeral on Wednesday. But as the Hutton inquiry prepares to sit for the first time tomorrow, it is unlikely the truce will hold. Whitehall insiders believe the Government will not demur from its strategy to undermine Dr Kelly's credibility. "They may well be more careful with their use of language, but the message will remain the same," a well-placed Whitehall source said.

Dr Kelly's family will receive little comfort, however, from the approach the BBC is likely to take in its bid to protect its journalists, its stories and its own reputation.

It is already clear that the BBC's legal team, headed by Andrew Caldecott QC, will seek to prove that Mr Gilligan's report was accurate - a strategy which, ultimately, will rest on disproving Dr Kelly's claims to managers at the MoD that the reporter had "considerably embellished my meeting with him".

The BBC, rather than questioning what Dr Kelly knew, will make its case by insisting that although Dr Kelly said he was "pretty sure" he had never spoken to BBC journalist Gavin Hewitt and that he had met his colleague, Susan Watts, only once, he was their source.

Ms Watts, it has emerged, tape-recorded the conversations with Dr Kelly that formed the basis of her reports for Newsnight.

Even Lord Hutton, a law lord, made it clear in his opening statement that the question of Dr Kelly's reliability when he gave evidence to the Commons Foreign Affairs Select Committee, two days before his death, would be an issue. The committee, after hearing him, erroneously concluded that he could not be the BBC's source. He was.

But questioning the reliability of remarks made by a worried man put on trial, his job hanging in the balance, is not the same as deliberately seeking to discredit the reputation of a man who spent his career as a respected, leading scientist latterly devoted to discovering weapons of mass destruction in Iraq. Whether that happens will be a matter for all involved in the Hutton inquiry to decide.