In the year 1685 a new charter was granted to the Trinity Company, and Pepys was named in it the first master, this being the second time that he had held the office of master.

Evelyn specially refers to the event in his Diary, and mentions the distinguished persons present at the dinner on July 20th.

It is evident that at this time Pepys was looked upon as a specially influential man, and when a parliament was summoned to meet on May 19th, 1685, he was elected both for Harwich and for Sandwich.  He chose to serve for Harwich, and Sir Philip Parker was elected to fill his place at Sandwich.

This parliament was dissolved by proclamation July 2nd, 1687, and on August 24th the king declared in council that another parliament should be summoned for November 27th, 1688, but great changes took place before that date, and when the Convention Parliament was called together in January and February, 1689-90, Pepys found no place in it.  The right-hand man of the exiled monarch was not likely to find favour in the eyes of those who were now in possession.  When the election for Harwich came on, the electors refused to return him, and the streets echoed to the cry of “No Tower men, no men out of the Tower!” They did not wish to be represented in parliament by a disgraced official.

We have little or no information to guide us as to Pepys’s proceedings at the period of the Revolution.  We know that James ii. just before his flight was sitting to Kneller for a portrait intended for the Secretary to the Admiralty, and that Pepys acted in that office for the last time on 20th February, 1688-89, but between those dates we know nothing of the anxieties and troubles that he must have suffered.  On the 9th March an order was issued from the Commissioners of the Admiralty for him to deliver up his books, &c., to Phineas Bowies, who superseded him as secretary.

Pepys had many firm friends upon whom he could rely, but he had also enemies who lost no opportunity of worrying him.  On June 10th, 1690, Evelyn has this entry in his Diary, which throws some light upon the events of the time:—­

“Mr. Pepys read to me his Remonstrance, skewing with what malice and injustice he was suspected with Sir Anth.  Deane about the timber of which the thirty ships were built by a late Act of Parliament, with the exceeding danger which the fleete would shortly be in, by reason of the tyranny and incompetency of those who now managed the Admiralty and affairs of the Navy, of which he gave an accurate state, and shew’d his greate ability.”

On the 25th of this same month Pepys was committed to the Gatehouse at Westminster on a charge of having sent information to the French Court of the state of the English navy.  There was no evidence of any kind against him, and at the end of July he was allowed to return to his own house on account of ill-health.  Nothing further was done in respect to the charge, but he was not free till some time after, and he was long kept in anxiety, for even in 1692 he still apprehended some fresh persecution.