It was a private session that ended acrimoniously with the committee chairman, Donald Anderson, holding an extraordinary impromptu press conference in the corridor in which he accused Mr Gilligan of changing his story over what happened at a meeting two months earlier between the journalist and Dr Kelly.
Mr Gilligan vigorously rejected the accusation and persisted in his refusal to name the source of his story that the dossier outlining the case for war had been "sexed up" by Downing St.
But Dr Kelly was never to hear of the outcome of the session, which he had known - from the news that morning - was to take place. He did not return from his walk. At 11.45pm his family called Thames Valley Police and reported that he was missing.
Yesterday at dawn a team of 70 police officers began a search. At 9.20am they found Dr Kelly's body in a densely wooded part of Harrowdown Hill, a Thames Valley Police spokesman said.
His family was devastated. His wife was too upset to say anything publicly, but told a family friend, the former BBC correspondent Tom Mangold, that her husband had been severely stressed by the whole affair.
"She told me he had been under considerable stress," Mr Mangold said, "that he wasn't well. She didn't use the word 'depressed', but she said he was very, very stressed and unhappy about what had happened and this was really not the kind of world he wanted to live in."
Southmoor village was in shock too. Neighbours who knew Dr Kelly, his wife, their daughter Sian, 32, and their twins Rachel and Ellen, 30, said they were a "lovely family".
Steve Ward, the landlord of Dr Kelly's local, the Hinds Head pub, said: "He was the most level-headed sensible person I've ever come across ... I can't believe that he would do anything like this."
Another villager said: "He never discussed his work, he was a straightforward family man - always a very nice person to talk to ... We're all greatly saddened."
But the news also sent ripples around the world. The Prime Minister was informed of the discovery of the body as he flew from Washington to Tokyo on his diplomatic marathon. He and his officials received the news in stunned silence.
The same response characterised the reaction of all sections of the political and news establishment embroiled in the prolonged row over the run-up to the war in Iraq.
Immediately, the blame game began as those involved sought to shrug off the recriminations to someone else.
Mr Anderson was quick to deny that the Foreign Affairs questioning of Dr Kelly had been too strong. "If it was strong, the criticisms appear to be more directed against the Ministry of Defence (MoD), rather than against him," the MP said.
"It wasn't as if he could be seen as a victim in the corner, or a person against whom a complaint was being made. So I don't think the questioning was aggressive against him ... I am sure that any objective person, looking at the transcript or listening to the hearing, would see that the tone was not aggressive at all."
The MoD promptly began briefing that Dr Kelly had at no point been threatened with suspension or dismissal as a result of his admission that he had spoken to Mr Gilligan. It was made clear to him at the time that he had broken civil service rules by having unauthorised contact with a journalist, but "that was the end of it", said a spokesman.
Downing Street too was keen to deny suggestions that the dead man had been made a "fall guy". A Number 10 spokesman insisted that Dr Kelly had come forward voluntarily with the information that he had met the BBC correspondent who had sparked the weapons row.
But everyone was clear that Dr Kelly's death had immense political implications, increasing political pressure for a full, independent judicial inquiry into the whole affair. That pressure will only be partly alleviated by Downing Street's announcement yesterday of a judicial inquiry focused just on the microbiologist's death, which will not be extended to cover the issue of the accuracy of the two dossiers making the case for war on Iraq.
The talk in Westminster was that the Defence Secretary, Geoff Hoon, would have to resign - or that the tragedy might hasten the departure of Alastair Campbell as Tony's Blair's head of communications. The BBC was facing accusations that had it confirmed that Dr Kelly was not the Gilligan source he might still have been alive.
Few people had thought the long, impenetrable saga - which one MP indelicately described yesterday as a "soap opera" - would end like this when on May 29 Mr Gilligan broadcast an item on the Today programme that a senior British official had told him that the Governments dossier on Iraq, published last September, was "sexed up" by Mr Campbell against the wishes of the intelligence services.
Within a month Mr Gilligan repeated the claim to the Foreign Affairs Committee inquiry on the Government's presentation of the case for war. A week later Mr Campbell, while giving evidence to the committee, aggressively denied the accusation and demanded an apology from the BBC.
When the committee's report was published on July 7, it cleared Mr Campbell - on the casting vote of the chairman - but pronounced that "undue prominence" was given to the dossier's claim that Saddam Hussein could launch weapons of mass destruction "within 45 minutes". At that point it seemed the story was all over bar the recriminations.
But then, the very next day, the MoD issued a statement announcing that an official - later named as Dr Kelly - had come forward to admit he met Mr Gilligan in the Charing Cross Hotel and discussed Iraq's weapons on May 22, a week before the original story was broadcast.
Dr Kelly, it emerged, had been part of the team that had helped draft part of the dossier, but only a section dealing with the history of UN inspections in Iraq.
The 59-year-old Oxford-educated microbiologist, originally with a background in agricultural science, had been scientific adviser to the MoD's proliferation and arms control secretariat for more than three years. He had risen through the ranks at the ministry's chemical research centre at Porton Down in Wiltshire to become head of microbiology.
He led all inspections of Russian biological warfare facilities and worked as senior adviser on biological warfare in Iraq after the first Gulf War and visited that country 37 times during seven years as a weapons inspector.
Why Dr Kelly came forward was unclear. It may have been that, as a member of the Commons' committee put it, his motives were "courageous and honourable".
He may perhaps have feared that he was about to be unmasked - he had been approached by the Sunday Times some weeks before and asked whether he was the BBC mole. Perhaps he was smoked out by pressure within the MoD, which would have been formidable, as anyone who has undergone a top civil service leak inquiry would testify.
Either way, the pressure was intense and Dr Kelly went to his bosses. For five days they are said to have grilled him. He told his line manager at the MoD that he may have been Mr Gilligan's source but that "on reflection" he had decided that what he told the journalist was so different from his report that he could not be the source.
Additional factors seemed to corroborate that. The reporter had admitted relying on a single source for his report, whom he describes as someone he had known for years and who did not work in the MoD - descriptions that did not fit Dr Kelly.
Mr Gilligan had made notes of their conversation on a PalmPilot, and yet the BBC man had testified that he had taken comprehensive notes during the meeting with his sources, which had been deposited with the BBC legal department.
But then five days later the MoD issued a rushed statement at 6.03pm announcing that an unnamed official had come forward to admit meeting the Today reporter.
Some commentators speculated that it had been timed to dilute media coverage of a Commons rebellion by Labour MPs over foundation hospitals, though the MoD later insisted that it had been issued so late because they had to track down Dr Kelly on his mobile and get him to pull into a motorway service station to agree to the wording of the statement.
Whatever the truth of that, the timing of the revelation - just a day after the Foreign Affairs Select Committee issued its ambiguous report clearing Mr Campbell but denouncing the "undue prominence" given to the 45 minutes claim - seemed panicky and political.
Though Dr Kelly had insisted he was not the source of the most controversial elements in the Gilligan story - a view with which the Committee agreed - and therefore not the BBC mole, the political spin put on the announcement implied that No 10 was "99 per cent convinced" that Dr Kelly was the mole.
So were political voices within the MoD.
The same idea hung in the air around the select committee hearing.
Journalists breathlessly reported how Dr Kelly was "barely audible" during his 20-minute grilling in Westminster. As temperatures soared outside on one of the hottest days of the year, a committee clerk switched off the noisy cooling fans so that the softly-spoken Government adviser could be heard. They wrote of how the silver-bearded, bespectacled man dressed in a pale green suit and tie, a visitor's pass hanging around his neck, sat with his head slightly bowed.
But though he told the committee that Mr Gilligan's account of his conversation with his source was so different from their conversation that he did not believe that he could be the source - and though the committee chairman, Mr Anderson, later wrote to the Foreign Secretary, Jack Straw, to say it seemed "most unlikely" that Dr Kelly was the journalist's source - the spin merchants seemed determined to make the mud stick.
The next day Ben Bradshaw, the hyper-loyalist Blairite junior environment minister, was still insisting that in the absence of a denial by the BBC it should be assumed that Dr Kelly was the mole. The BBC claimed that it was all a Downing Street "trick" to root out their real source.
It all took its toll on the unhappy scientist. As did the way he continued to dwell on what he saw as the unfairness of the intense questioning by MPs on the committee.
At one point Labour's Andrew Mackinlay had thundered angrily at the scientist: "This is the high court of Parliament and you are under an obligation to reply!"
He then said to Dr Kelly: "I reckon you're chaff. You've been thrown up to divert our probing. Have you ever felt like the fall guy? I mean, you've been set up haven't you?"
Dr Kelly had replied: "That's not a question I can answer."
When the MP said: "But do you feel that", Dr Kelly said, "No, I accept the process that's going on."
And when the Conservative member, Sir John Stanley, said: "You were being exploited to rubbish Mr Gilligan and his source, quite clearly", Dr Kelly could only shrug and say, "I've just found myself in this position out of my own honesty of acknowledging the fact that I had interacted with him."
One MP detected how unhappy Dr Kelly was at what was happening to him. The Tory committee member Richard Ottaway, who said people like Dr Kelly were not used to the pressure faced by MPs on a day-to-day basis, said: "He did give a hint of the pressure he was under when he said he was unable to get to his house at the moment because of the media intrusion."
Yet, privately, it was clear the impact all this had on Dr Kelly. His wife has told family friend Mr Mangold that her husband was infuriated and made deeply unhappy at how events had unfolded. "
She told me that he was very, very angry about what had happened at the committee," Mr Mangold said, "that he wasn't well, that he had been to a safe house, he hadn't liked that, he wanted to come home."
Last night the theories were rebounding around Westminster.
Did Dr Kelly's death imply that he really was Mr Gilligan's mole and could not bear the remorse of having lied?
Had Mr Gilligan exaggerated or been misled about Dr Kelly's role?
Or had Mr Gilligan genuinely had another source, and had the pressure on Dr Kelly came from elsewhere - perhaps the fear that he might be recalled for yet another grilling by the Foreign Affairs Select Committee.
Whatever the truth, there can be little doubt that the pressure of events combined to a level intolerable for Dr Kelly - and that a good man and faithful public servant died as yet more collateral damage of this questionable war and the spin used to distract public attention away from the real issues of whether war was justified.
During a lecture on his role as a senior UN adviser on biological warfare he once said: "When Iraq invaded Kuwait in August 1990, little did I realise that Saddam Hussein would dictate the next 10 years of my life."
Nor did he realise it would dictate the course of his death.
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INDEPENDENT
British Parliament Foreign Affairs Committee transcript:
Evidence of Dr David Kelly
Key players in the 'sexed-up dossier' affair
Herald Feature: Iraq
Iraq links and resources
