The outbreak of plague began slowly in the spring, accelerated in the summer. and peaked in September. It declined during the late fall. By early 1666 it was all but over. By then it had killed @100,000 people out of a pre-plague population of @450-500,000. At its height in September, 7000 deaths per week were recorded, but that was surely an undercount. Many deaths went unreported.
Nearly half the people fled London during the epidemic, obeying what was thought to be the best prescription of the time: "Flee from the infected." Thus, the mortality rate among those who remained was probably close to 50%. The royal government did not make any attempt to stop the exodus. In fact, the king and his court fled, to Salisbury, then to Oxford.
Fleeing was more feasible for people of means: aristocracy, gentry, and wealthy merchants and professionals, including clergymen and physicians. Most of them had houses in the country, or relatives they could stay with. The physicians could do little against the plague; staying would have had little impact.
People below those groups fled as well, but they often had no fixed place to go. Inhabitants of villages and towns in the areas outside London often chased them away, fearing the spread of the infection. Many people were forced into the woods, to beg, steal, scavenge, and sometimes die of starvation or exposure.
The plague spread anyway, although not as much as during the Black Death of the 14th century. One of the most famous places it spread to the was the tiny village of Eyam, whose inhabitants quarantined themselves to protect nearby villages and towns, at great cost to themselves.
To their credit, the Lord Mayor and most city officials remained at their posts. The city distributed some food aid to the people. Farmers from the nearby countryside brought food. They left it outside the city gates, and negotiated prices at a distance. People who came to buy collect it left coins in buckets filled with water to disinfect them.
There was no official "lockdown" but people were urged to keep their social distance. Just as today, many people refused to observe sensible precautions. The diarist Samuel Pepys recorded with dismay that people continued to gather in businesses and shops and attend large funerals. One evening he stood looking longingly at a jolly group of people socializing in a tavern, but turned away, having decided he did not wish to die for a drink.
The authorities ordered the building of temporary pest houses to quarantine the infected, who would have overwhelmed the few hospitals. The city also employed mandatory house quarantine. Whenever the infection broke out in any household, everyone in the house was shut up with the sick person, which could be a death sentence for all the residents. Crosses would be painted on the house doors to warn others away.
Contemporaries recalled hearing the screams of the sick and terrified in the shut up houses. People naturally tried to escape these confinements, so guards were posted outside the houses to prevent it. Rioters sometimes broke open the houses and released the residents. Sometimes the guards were bribed to let the residents escape. Most shops eventually closed, because their owners had fled or died.
The streets were eerily quiet except for the dead carts going around to pick up the dead, who were often dumped in mass graves. Grass began to grow in the streets due to the lack of traffic.
As the number of deaths mounted, the authorities closed alehouses and limited the number of lodgers who could stay in a household. They ordered a cull of cats and dogs, in the belief that they might carry the plague. That probably made things worse, since these animals killed many rats, whose fleas were major transmitters to humans. The city government also ordered the burning of fires in the streets, based on the widespread belief that miasma, or bad air, was the cause of the disease. The fires were supposed to disinfect the air.
One of the best accounts of the Great Plague of 1665 in London is a work of fiction. Daniel Defoe wrote The Journal of the Plague Year in 1721. It was what we would call a potboiler today, written due to heightened interest in and fear of plague. A major epidemic of plague had broken out in Marseilles, France, and it was commonly believed that it would move on to London. In the event it did not. The 1665 plague was the last major outbreak in the UK.
Despite being fictional, Defoe's work was soundly based on official documents, eyewitness reports, and a few short written accounts. Defoe lived in London at the time of the plague, although he was only five years old at the time. His uncle, Henry Foe, may have been a major source of information. Foe stayed in London throughout the plague. He was a saddler. Defoe's narrator in the journal is a saddler. At the end of the book are the initials "HF."
The contemporary woodcut below provides some sense of Londoners' experiences during the Great Plague. Death is everywhere, even following those who flee the city. On the far right, those fleeing are being stopped by armed countryfolk telling them to keep out.
As if London hadn't been punished enough, the following year brought the Great Fire of London. The fire raged for five days, between September 2-6 and destroyed 4/5ths of the city inside the old Roman Wall, including St. Paul's Cathedral and 87 parish churches. Amazingly, only six people were killed.
Further Reading: A. Lloyd Moote, Dorothy C. Moote, The Great Plague: The Story of London's Deadliest Year (Baltimore: Johns Hopkins University Press, 2004).