The Emperor's Gold, Robert Wilton's brilliant debut historical novel is on the verge of publication. Set in 1805 as Napoleon prepares to invade Britain, the action and intrigue is propelled by the strange career and exploits of one man, the dark and ambiguous Tom Roscarrock. But perhaps the real story is the organisation moving, appropriately enough, in the shadows behind him: the mysterious Comptrollerate-General for Scrutiny and Survey.

The Comptrollerate-General's activities have only come to light through the chance discovery of an archive of documents in the basement of the Ministry of Defence, in London. Author Robert Wilton describes the moment in his introduction to The Emperor's Gold, which is the first of a series of books that will draw on the archive to illuminate a particular crisis or phase in British history. "But it's hard to do justice to the discovery," he says now. "Going through files in a basement isn't exactly James Bond stuff. Then, as I flicked through the papers, the most extraordinary mix of names started to crop up, and these strange tangential allusions to significant but apparently unrelated bits of history - anything from the massacre at Glencoe to the Russian Revolution. At that moment, of course, I had no idea what I'd stumbled across," he recalls. "To be honest, I probably still haven't."

It's clear from the archive that the Comptrollerate-General has been operating behind the scenes of British Government for more than four centuries. It seems to have been involved, in one way or another, in the most crucial periods of threat, tension and controversy in the country's history. The archive apparently includes a manuscript letter from 1553 referring to the doomed attempt to install Lady Jane Grey as Queen of England; there's also supposed to be a type-written correspondence about the bizarre flight of Rudolf Hess, one of Hitler's closest confidants, to Scotland at the height of the second world war.

Amazing stories come out of the archive - the extraordinary intrigues and bloodshed described in The Emperor's Gold, taking place in the months before the battle of Trafalgar in 1805, are just one, and Wilton drops tantalising hints about the organisation's activities in the American war of independence, and something called the Great Pomeranian Fiasco - but the Comptrollerate-General itself, its structures and systems, remains a mystery.

"Half the time it's not even clear who the head of the organisation is," Wilton comments, "let alone how he's running it or what he's up to." But where the archive does give indications, they show a remarkable cross-section of men. "Lord Hugo Bellamy, the Comptroller-General who features in The Emperor's Gold, was obviously extremely impressive: a huge man physically, who rose to one of the most influential positions in government by sheer ruthless ability and exceptional intelligence. Another man is only ever referred to as Lamprey, which I guess is a cypher - more than one chief used them in all correspondence - and I think that one of the pre-20th Century Comptrollers-General may actually have been a woman. And then of course there's Knox."

Colonel Valentine Knox was Comptroller-General around the end of the first world war, and the man responsible for assembling the archive that Robert Wilton found nearly a century later. 'The most dangerous man in Europe', was how one subordinate described him. 'He gave the distinct impression that he spent breakfast considering whether to fight the day for England or for Germany.'

His methods did not go down well. The archive includes a letter from Sir Henry Wilson, subsequently Chief of the Imperial General Staff, to the Secretary of State for War, complaining at the Comptrollerate-General's - or in particular Knox's - lack of proper bureaucratic transparency, and lack of scruple. "Uncontrolled, unprincipled, and unenglish," he wrote, "Colonel Knox's Department of Scrutiny and Survey, both in its casual, amateurish organisational principles and in its disreputable manner of warfare, is a strategic danger both to the proper management of our security affairs and to our international reputation. Knox claims that his late operations in the Levant may have won us the holy lands; to those few who know of them, they have lost us all moral advantage over our foes, and the name of gentlemen."

Knox seems to have kept the letter as a kind of trophy (one wonders how he acquired it), but the unjustified accusation of amateurishness apparently stung, and his subsequent antipathy to the significantly more senior Wilson was well-known. Sir Henry Wilson was assassinated in 1922. The Comptrollerate-General for Scrutiny and Survey endured.