Shortly afterward, in 1971, he was recruited by MI6 and served in Moscow, Nairobi (1973–1976), and Paris. In 1994, after a tit-for-tat row between the British and Russian authorities, Scarlett was expelled from Moscow where he had been MI6's station chief.[6] He later became Director of Security and Public Affairs.[7]
The normally secretive intelligence services were thrust into the public gaze in the Summer of 2003 after the death of the eminent government weapons expert, Dr David Kelly. Kelly had been found dead in the Oxfordshire countryside near his home, after being exposed as the source of allegations that the government had "sexed-up" intelligence regarding existence of weapons of mass destruction in Iraq prior to the 2003 invasion of Iraq. The "classic case" was the claim that Iraq could launch Weapons of Mass Destruction "within 45 minutes of an order to do so"—Dr Kelly had privately dismissed this as "risible".[9]
Scarlett gave evidence at the Hutton Inquiry into the circumstances surrounding Kelly's death.[10] It became clear that Scarlett had worked closely with Alastair Campbell, then British Prime Minister Tony Blair's Director of Communications and Strategy, on the controversial September Dossier, with Campbell making drafting suggestions which the inquiry found may have "subconsciously influenced" Scarlett and the JIC. This influence may have had deleterious effects on the quality of the assessments presented in the dossier. For instance, the Intelligence and Security Committee of Parliament made several criticisms in their report "Iraqi Weapons of Mass Destruction: Intelligence and Assessments":
"As the 45 minutes claim was new to its readers, the context of the intelligence and any assessment needed to be explained. The fact that it was assessed to refer to battlefield chemical and biological munitions and their movement on the battlefield, not to any other form of chemical or biological attack, should have been highlighted in the dossier. The omission of the context and assessment allowed speculation as to its exact meaning. This was unhelpful to an understanding of this issue."[11]
Scarlett became the head of SIS on 6 May 2004, before publication of the findings of the Butler Review.[12] Although the review highlighted many failings in the intelligence behind the Iraq war and the workings of the Joint Intelligence Committee, it specifically stated that Scarlett should not resign as head of the Committee and SIS.[13]
On 8 December 2009, Scarlett gave evidence to the Iraq Inquiry. He denied he was under any pressure to "firm up" the September Dossier, and claimed there was "no conscious intention" to mislead about Iraq's weapons but it would have been "better" to have clarified battlefield munitions not missiles were meant.[14]
On 26 June 2011, The Guardian reported on a memo from Scarlett to Blair's foreign affairs adviser, released under the Freedom of Information Act 2000, which referred to "the benefit of obscuring the fact that in terms of WMD Iraq is not that exceptional". The memo has been described as one of the most significant documents on the September dossier yet published as it is considered a proposal to mislead the public.[15]
MI6 – A Century in the Shadows (Part Three), 31 December 2010, 24:00, "In the final part of this series, Sir John Scarlett, the former head of Britain's Secret Intelligence Service talks about the interrogation of terrorist suspects and MI6's role in the run up to the war in Iraq."