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Today's final hearing saw bitter criticism of the Ministry of Defence from the Kelly family, and an equally strong attack on the BBC by the lawyer representing the government.
The inquiry has spent six weeks hearing evidence from more than 70 witnesses, including the Prime Minister, Tony Blair, and key figures from the BBC and the intelligence services.
Lord Hutton will now consider his report, and says he hopes to present his findings later this year.
The inquiry has been looking into the circumstances surrounding the apparent suicide of Dr Kelly, soon after he was named as the suspected source of a BBC report claiming the government "sexed up" a dossier on the threat from Iraq.
The first to speak was the Kelly family's lawyer, Jeremy Gompertz QC.
He outlined the two main outcomes the family wants from the inquiry:
"One - that the duplicity of the government in their handling of Dr Kelly should be exposed; and two - that the systemic failures at the Ministry of Defence should be identified and remedied so as to ensure as far as is humanly possible that no-one else should suffer the ordeal endured by Dr Kelly."
The Defence Minister, Geoff Hoon, has been under increasing pressure to resign over the role of his department, which ultimately confirmed Dr Kelly's name to the press.
Jonathan Sumption QC, for the government, strongly criticised the BBC, saying the Corporation had never acknowledged how serious the allegations it broadcast really were.
The BBC, he said, "seemed to have regarded this as a routine piece of political mudslinging, chatter in the air".
However, the BBC's lawyer, Andrew Caldecott QC, pointed out that Dr Kelly had spoken to three separate journalists at the BBC about his concerns that the Iraq dossier had been subject to "political interference".
He said the BBC did not present the criticisms as true, but it did present them as credible.
"That broad judgement, the BBC defends as entirely right," Mr Caldecott said.
Lord Hutton published his report on 18 January 2004.
He was highly critical of BBC governors for failing to investigate properly Downing Street's complaints.
As a result, the BBC chairman Gavyn Davies, the corporation's Director General, Greg Dyke, and reporter Andrew Gilligan resigned.
Lord Hutton absolved the government of any kind of "dishonourable, underhand or duplicitious strategy" in the leaking of Dr Kelly's name to the press.
But he said the Ministry of Defence was "at fault" for failing to tell Dr Kelly that his identity as the suspected source would be confirmed to journalists who suggested it.
He said Mr Gilligan's report that the Iraq dossier was sexed up was "unfounded" and that Joint Intelligence Committee chairman John Scarlett had acted to ensure the dossier was consistent with reliable intelligence.
In June 2004, the BBC published an internal review of its journalism. The Neil Report recommended a new emphasis on the training of journalists.
The following month, the government came under further pressure over its decision to go to war in Iraq as the Butler Report criticised the "thinness" of the intelligence used to justify the war.
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