For the first few months of his diary-keeping, Pepys was preoccupied with General George Monck and his march towards London. Perhaps this preoccupation was designed to keep his mind away from the problems that he was having in his marriage; she deeply resented his long absences, and so his leaving to accompany Montagu's fleet on their trip to the Netherlands to fetch the exiled king Charles II back to London probably made his domestic situation far worse. For their efforts, the men were well-rewarded by the king; Montagu with a title, Peps with a position as Clerk of the Acts - also known as keeper of the King's secrets - to the Navy Board, one of the most important positions that a civilian could hold at the time. The position came with a salary of three hundred and fifty pounds, and that didn't include bribes, backhanders and incentives, although Pepys records that he rejects an offer of one thousand pounds from another man who also wanted the job. He and his wife shortly moved from their home to the official residence of the Clerk of the Acts, a rather nice house on Seething Lane in the heart of the City of London.
Pepys goes into great detail about the Second Anglo Dutch War, which began in 1665. His colleagues were proving good at their jobs only in peace time and so a great deal of responsibility fell on his shoulders. He suggested a centralized approach to supplying the fleet with what they needed and due to the popularity of this play, he notes that he was made Surveyor General of Victuals, a role which also added to the Pepys coffers, paying an additional three hundred pounds a year. Pepys was realistically negative about the outcome of the war, noting that the Dutch had the measure of the English navy.
Pepys was proved right; the English lost the war on the water, and began to advance into England on the land. Pepys details the Raid on the Medway in the county of Kent, observing that the fortress of Upnor Castle that had been intended to defend the shoreline and the troops from invaders was woefully inadequate. The Dutch stole the Royal Charles, one of the Royal Navy's most important ships. Pepys, ever the pragmatist, took both his wife and his gold out of London, for safe keeping.
Pepys felt himself under growing scrutiny from Parliament. They demanded that he make a list of all of the commanders who had reneged in their duties, but Pepys did not mind doing this because none of these men were actually in is charge, and so he was able to comply with the orders of Parliament without putting himself in a bad light at all. However, in 1669 he was called before the parliamentary commission to prepare answers to their detailed questions, and had to defend his own role. Again, because of the King's great debt to him, he was able to come out of the episode relatively undamaged.
Pepys was not amongst those at enormous risk of catching the plague, which occurred quite regularly in London. His living accommodations were spacious and clean; he did not mix with poor people, or find himself unable to get out of London if he had to for his own health and wellbeing. All that being said, he did not tend to give much more than a cursory diary entry to outbreaks of the plague; all that changed in June 1665, when the plague seemed unusually severe. Ironically, plague year had started out as one of the best years of Pepys' life, and he paid little attention to the plague until the middle of the year. Although he enjoyed considerable merriment that year, he was saddened by what he saw going on around him; empty streets, conscious of buildings that seemed too boarded-up in case plague carriers were hidden away behind the doors. Pepys also worried enormously that his wigs might be contaminated; what if wig-makers were using the hair of those who had perished from the plague? Although the plague did not put a dent in his enjoyment of life, it did curtail his activities somewhat. He moved the Navy Board offices to Greenwich, out of the city, and he sent his wife to Woolwich. By January 1666, there were three hundred additional graves in the churchyard at St. Olave's, opposite the Pepys' window.
1666 did not prove to be a much better year for the dwellers in the city of London. On September 2, Pepys' servant woke him up in the early hours and told him that he could see a fire in the Billingsgate area of the city, famous for its fish markets. He went back to bed - after all, Billingsgate was near the Thames and a fire was unlikely to break out when surrounded by water. Pepys' logic was deeply flawed; his servant came back to the house later that morning and informed him that three hundred houses had been burned to the ground and that now London Bridge was under threat. Pepys hurried to the Tower of London, adjacent to the Bridge, in order to get a better understanding of what was happening. He went down to the water and got into a boat, so that he could get as close as possible to the Bridge. He saw that the Old Swan pub was burning. He saw that the steel traders were racing against time to remove their goods. He was also struck by the pigeons who did not understand the danger that they were in and remained in their nests, loath to leave them. He also observed that there were so many people trying to remove their belongings and get into any available boats to safety that nobody was actually trying to put the fire out at all. There had been a drought, very uncharacteristic in gloomy London, and everything was dry. Even the church was starting to burn. He watched as the steeple fell. Pepys took the boat towards Whitehall and told the king of the fire. He recommended that homes that were in the path of the fire be pulled down in advance so that the fire could not use them as fodder or kindling. The king agreed and Pepys went to the Lord Mayor on foot because the streets were impossible to traverse. However, the Lord Mayor had already thought of this and had been pulling houses down; it was not working and the fire was still gaining ground and strength.
Pepys went home in the middle of the afternoon and enjoyed an extremely good dinner with great company, but afterwards returned to watch the fire which was now advancing even to threaten his own home. He and his wife packed up their belongings, which he sent to a friend in Bethnal Green, east London. He ate leftovers for dinner, a pretty poor state of affairs for a man who considered himself a gourmand. He bemoaned the absence of condiments and dressings. He was also working himself into a frenzy about Seething Lane as a whole and wanted all of the homes pulled down. When the fire reached the end of the lane, Pepys sent his wife, and his gold, to Woolwich. Things were getting very bad in the city; there was looting, and more violence than usual. St. Paul's Cathedral was in ruins, as was his alma mater, his childhood home, and his neighbors' homes.
Pepys managed to save his many musical instruments, which was fortunate because he was a man of music and the arts. He was also a man who loved the company of others, a bon viveur, and a connoisseur of food. He tells in detail of the flageolet lessons he and his wife took together. He was also a jealous man when it came to his wife, despite a relationship that could sometimes be difficult. He describes how he had curtailed her dancing lessons because the dancing teacher was showing all together too much interest in her.