The years 1665 and 1666 are two of the most devastating London ever saw, being the dates of the Great Plague followed by the Great Fire.
But plagues don’t come out of nowhere. Like any disease that affects large numbers of people, they have their cycles and – since they are now largely wiped out, they are largely preventable.
Bubonic Plague had visited England many times, and is described to have been ‘naturalised between the years 1636 and 1647 in London. It was virtually eradicated by 1648, and there were no outbreaks during the Commonwealth at all. But within 5 years of the Restoration of the Monarchy, it returned in its most virulent outbreak ever.
I am sure that if anyone at the time was counting these outbreaks, they would have attributed it to the wrath of god on the godless population, a sure sign he had smiled on those who had risen up against the king, but the absence of it between 1648-65 represents virtually a generation in those days, who had grown up with no exposure to the illness, so became exceptionally vulnerable to it when it returned.
There are probably other factors involved here, such as the plain lifestyles of the puritans, as opposed to the unhealthy food and degenerate lifesyle of the Royalists.
Cromwell was famously an army man, who neglected the navy, and there was a slump in overseas trade during his time, so less opportunity to import diseases in general.
There is a description of the Great Plague by one of the non conforming ministers who stayed in London whilst the established churchmen (ie the Anglicans) had fled:
“Now people fall as thick as the leaves in autumn when they are shaken by a mighty wind. Now there is a dismal solitude in London streets; every day looks with the face of a Sabbath day, observed with a greater solemnity than it used to be in the city. Now shops are shut in, people rare and very few that walk abut, insomuch that the grass begins to spring up in some places, and a deep slilence in every place, especially within the walls.”
And for al the claims that Bartholomew Fair was by then becoming a godless place, the Great Fire happened on the eve of it the following year, though it had been cancelled as the plague risk remained. The fire stopped at Pye corner, at the edge of the fair ground.