The Plot Against Pepys, By James Long and Ben Long

Years after he closed his diary, Samuel Pepys had to use all his ingenuity and courage to outwit a deadly enemy

At the zenith of his career as a bureaucrat in the service of King Charles II, in 1679, Samuel Pepys was accused of treason and imprisoned in the Tower of London. He soon discovered that there was a plot against him, hatched by a vicious fantasist named Colonel Scott and eagerly taken up by his Whig enemies. It was a sub-plot of the better-known Popish Plot, which was fabricated by another vicious fantasist named Titus Oates. He had claimed that a group of Catholic citizens intended to overthrow Charles II and replace him on the throne with James, Duke of York, his Catholic-convert brother. Pepys, who had served as Secretary of the Navy while the Duke of York had been First Admiral, was falsely accused of being a secret Catholic and of supplying naval secrets to French government officials. By attacking Pepys as a traitor, his enemies in Parliament were attacking the Duke of York by proxy.

Historians have so far overlooked this dastardly and abortive intrigue, perhaps because Pepys is more celebrated for his diary, which he had ceased keeping in 1669 owing to the strain on his eyesight. The father-and-son team of James and Ben Long have now rectified this omission, furnishing us with a historical investigation that has all the vigour and panache of superior detective fiction.

It all started a few months after Oates first unleashed his accusations, when Justice Edmund Godfrey was found murdered on Primrose Hill in October 1678. Oates sensationally claimed that he had been killed because he knew too much about the Catholic plot. As Secretary of the Navy and Justice of the Peace in Kent, Pepys took an interest in a suspicious individual who was hanging around Gravesend, seeking passage across the Channel. Might this man be Justice Godfrey's assassin? By the time an arrest warrant was issued he had sailed for France. He turned out to be one Colonel John Scott. Already nursing a resentment against the Duke of York, he would never forgive Pepys for ordering a search of his lodgings in Cannon Street and seizing his belongings and some of his money. He plotted a swift revenge.

After a couple of months' imprisonment in the Tower, Pepys secured his release by invoking the newly created concept of Habeas Corpus, though the bail required was onerous to his friends. He then deployed a network of agents to disprove Scott's claims and to gather information about his mendacious character. This was to prove a costly and time-consuming business; since sworn affidavits were not admissible at trial, Pepys would have to arrange for foreign witnesses to be brought over from France and Holland at his expense and give evidence in person.

Colonel Scott, it turned out, was a consummate rogue. Brought up in the American colonies, he realised he could exploit the ignorance of the mother country. His first crime had been selling some land he didn't own to a wealthy London family. Styling himself as a captain – although he had never undertaken military service – and inventing noble antecedents, he returned to the American colonies in the 1660s, where he used a forged royal instrument to commandeer land, took money in return for bogus promises to obtain royal charters and lobbied London to be made Governor of Long Island until the Duke of York intervened.

Once exposed as a fraud, Scott headed for the Caribbean, where he took part in a military expedition against the French on St Kitts and was excoriated for his cowardice in battle. From there he moved to Holland, where he was promoted to the rank of colonel in the Dutch army as a reward for charging an official with embezzlement – falsely, as he had been the embezzler. This was followed by a fleeting period as a spy for Charles II's government against his Dutch hosts. Before long, say the authors, Scott "was at the end of his tether, addicted to the pursuit of greatness but exhausted by it, and a wanted man in every part of the world he had spent time in". But still he ploughed on. In France, he formed a partnership with a cannon founder and attempted to sell King Charles's gun-making secrets to the French crown. In other words, he contrived to accuse Pepys of the very crime he had contemplated himself.

Before the treason case against Pepys could go to trial it started to unravel; Colonel Scott was also wanted for the murder of a hackney-carriage driver who had troubled him for his fare while Scott was in his cups.

James and Ben Long (the former has 11 novels to his name and the latter is a theatre director and budding playwright) have illuminated a murky episode in British political history. At the core of this book is a duel of wits between a royal bureaucrat, who works doggedly and meticulously to establish his innocence, and an unscrupulous chancer, who becomes the willing vessel of a group of Whig politicians. The atmosphere of London during the Popish Plot is deftly conveyed, each page being charged with a sense of the danger in which Pepys found himself and the courage with which he faced it.

Pepys was denied the satisfaction of seeing Scott exposed in the courtroom and convicted for perjury. But unlike Pepys, the reader discovers that when Scott had first come to Pepys's attention at Gravesend he had actually been on a treasonable mission to the French king on behalf of the Duke of Buckingham, who had in mind to overthrow Charles II and take his place. Accordingly, the Longs believe that "Scott and Buckingham together were surely the originators of the plot against Pepys."

Pepys's career revived. Scott, on the other hand, faded from the feverish scene of Restoration London, still wanted for the murder of the hackney-carriage driver. He returned to the Caribbean and eventually secured a role in the minor reaches of colonial officialdom, as Speaker of the Montserrat Assembly. For a while though, he had come close to destroying Samuel Pepys.