Kelly inquiry: The case against the Ministry of Defence

If heads roll over the David Kelly affair then Geoff Hoon, the Secretary of State for Defence, and some of his senior civil servants are the most likely casualties.

It was the Ministry of Defence press office that confirmed Dr Kelly's identity to the media, and it was ministry officials who had direct dealings with him from the time he came forward to admit his contact with Andrew Gilligan up to his apparent suicide. What exactly happened in that crucial period remains unclear.

What we do know is that on 9 July, nine days after Dr Kelly told his superiors about his meeting with Mr Gilligan, Richard Hatfield, the personnel director at the MoD, wrote to Dr Kelly saying that his behaviour had fallen well short of the standard that he would have expected. Mr Hatfield had ended his note by saying that despite this, it would not be "appropriate" to initiate formal disciplinary proceedings.

But were any verbal threats of sanctions made against the scientist? The MoD has denied that Dr Kelly was threatened with being charged under the Official Secrets Act or the loss of his pension. But, according to Whitehall sources, there was talk of him losing his security clearance.

MoD officials approached the Intelligence and Security Committee and said the committee might want to interview Dr Kelly. At the same time, the scientist was asked whether he would agree to appear.

Dr Kelly was told that his appearance before the committee would be in camera and that his identity would be protected. According to a number of sources, Sir Kevin Tebbit, the ministry's most senior civil servant, is said to have agreed to this formula but was overruled. It is not clear whether he was overruled by Mr Hoon or Downing Street, or - more likely - Mr Hoon acting on instructions from Downing Street.

On the evening of 8 July, just in time for the main television news bulletins, the MoD issued a statement saying an official had come forward to say that he had met Mr Gilligan. On the following day, the MoD gave enough hints to journalists, including the crucial fact that he had been an UN inspector in Iraq, to put Dr Kelly in the frame. Downing Street, however, took the added precaution of leaking his name to three sympathetic journalists. The name was confirmed to the three newspapers by the MoD press office later in the day.

So Dr Kelly's name was out, with the finger of suspicion pointed firmly at the MoD. There is strong feeling at the ministry, however, that the whole process was set up by Downing Street.