Murder on High Holborn / Susanna Gregory.

Enhanced descriptions from Syndetics:

In 1665 England is facing war with the Dutch and the capital is awash with rumours of conspiracy and sedition. These are more frenetic than normal because of the recent sinking in the Thames of one of the largest ships in the navy - a disastrous tragedy that could very well have been caused by sabotage.

As an experienced investigator, Thomas Chaloner knows that there are very few grains of truth in the shifting sands of the rumour-mill, but the loss of such an important warship and the murder of Paul Ferine, a Groom of the Robes, in a brothel favoured by the elite of the Palace of White Hall makes him scent a whiff of genuine treason.

As well as investigating the murder, Chaloner is charged with tracking down the leaders of a fanatical sect known as the Fifth Monarchists. He suspects his masters are not particularly concerned by their amateur antics, and that the order for him to infiltrate the group is intended to distract him from uncovering some unsavoury facts about Ferine and his courtly associates.

Then, as he comes to know more about the Fifth Monarchists and their meetings on High Holborn, he discovers a puzzling number of connections - to both Ferine's murder and those involved with the defence of the realm. Connections that he must disentangle before it is too late to save the country ...