When Charles II returned from exile following the Civil War and Commonwealth period Pepys was part of the entourage that sailed to Holland to bring back to England the King and his brother James. Later that year Pepys witnessed the spectacle of Major General Harrison, a Parliamentarian and signatory of the execution of Charles I, being hung, drawn and quartered at Charing Cross.
For his part in the return of the monarch Montagu was elevated to become Earl of Sandwich and he found Pepys a new role as Clerk of the Acts of the Navy Board. The Clerk was one of the four principle officers responsible for the administration and equipping of the entire naval fleet, along with their staff of commissioners and clerks. They reported to the Lord High Admiral, who by then was the King’s brother James, the Duke of York. In July 1660 Samuel and Elizabeth moved into a splendid apartment within the Navy Board building at Seething Lane on the north-east side of Tower Hill, where they were to live for many years.
Pepys immersed himself in learning the workings of the navy, spending much time at Deptford and Woolwich to understand every detail of the royal dockyards. The navy had grown in size during the Interregnum and by the time he joined the Board accounted for one quarter of all government spending, supporting a large part of the country’s industry. With such a great level of expenditure and a large number of suppliers Pepys soon found that the navy was riddled with corruption at almost every level. He spent much of his career reforming practices, while at the same time not averse to occasionally lining his own pockets. The navy also faced a continual financial crisis, an issue that was to dominate much of his career.
A national disaster occurred with the devastation by the Dutch of the laid-up English fleet in the Medway in June 1667. The debacle was a great shock to the nation and Parliament wanted answers as to how it had occurred. Fingers were pointed in the direction of the Navy Board, with Pepys having to defend his department at an inquiry in October 1667. He and his colleagues were called before Parliament in March 1668. Pepys delivered a masterful three-hour long speech that senior politicians agreed was the best they had ever heard in the House. The following day when he chanced upon the King and Duke of York in the park they congratulated him on his great success.