Pepys was put to great expense in collecting evidence against Scott and obtaining witnesses to clear himself of the charges brought against him. He employed his brother-in-law, Balthasar St. Michel, to collect evidence in France, as he himself explains in a letter to the Commissioners of the Navy:—
In the end Scott refused to acknowledge to the truth of his original deposition, and the prisoners were relieved from their bail on February 12th, 1679-80. John James, a butler previously in Pepys's service, confessed on his deathbed in 1680 that he had trumped up the whole story relating to his former master's change of religion at the instigation of Mr. William Harbord, M.P. for Thetford.
Pepys wrote on July 1st, 1680, to Mrs. Skinner:
William Harbord, of Cadbury, co. Somerset, second son of Sir Charles Harbord, whom he succeeded in 1682 as Surveyor. General of the Land Revenues of the Crown, was Pepys's most persistent enemy. Several papers referring to Harbord's conduct were found at Scott's lodging after his flight, and are now preserved among the Rawlinson MSS. in the Bodleian. One of these was the following memorandum, which shows pretty plainly Pepys's opinion of Harbord:—
Besides Scott's dishonesty in his dealings with Major Gotherson, it came out that he had cheated the States of Holland out of L7,000, in consequence of which he was hanged in effigy at the Hague in 1672. In 1682 he fled from England to escape from the law, as he had been guilty of wilful murder by killing George Butler, a hackney coachman, and he reached Norway in safety, where he remained till 1696. In that year some of his influential friends obtained a pardon for him from William III., and he returned to England.
In October, 1680, Pepys attended on Charles II. at Newmarket, and there he took down from the King's own mouth the narrative of his Majesty's escape from Worcester, which was first published in 1766 by Sir David Dalrymple (Lord Hailes) from the MS., which now remains in the Pepysian library both in shorthand and in longhand? It is creditable to Charles II. and the Duke of York that both brothers highly appreciated the abilities of Pepys, and availed themselves of his knowledge of naval affairs.
In the following year there was some chance that Pepys might retire from public affairs, and take upon himself the headship of one of the chief Cambridge colleges. On the death of Sir Thomas Page, the Provost of King's College, in August, 1681, Mr. S. Maryon, a Fellow of Clare Hall, recommended Pepys to apply to the King for the appointment, being assured that the royal mandate if obtained would secure his election. He liked the idea, but replied that he believed Colonel Legge (afterwards Lord Dartmouth) wanted to get the office for an old tutor. Nothing further seems to have been done by Pepys, except that he promised if he were chosen to give the whole profit of the first year, and at least half of that of each succeeding year, to "be dedicated to the general and public use of the college." In the end Dr. John Coplestone was appointed to the post.
On May 22nd, 1681, the Rev. Dr. Milles, rector of St. Olave's, who is so often mentioned in the Diary, gave Pepys a certificate as to his attention to the services of the Church. It is not quite clear what was the occasion of the certificate, but probably the Diarist wished to have it ready in case of another attack upon him in respect to his tendency towards the Church of Rome.
Early in 1682 Pepys accompanied the Duke of York to Scotland, and narrowly escaped shipwreck by the way. Before letters could arrive in London to tell of his safety, the news came of the wreck of the "Gloucester" (the Duke's ship), and of the loss of many lives. His friends' anxiety was relieved by the arrival of a letter which Pepys wrote from Edinburgh to Hewer on May 8th, in which he detailed the particulars of the adventure. The Duke invited him to go on board the "Gloucester" frigate, but he preferred his own yacht (the "Catherine "), in which he had more room, and in consequence of his resolution he saved himself from the risk of drowning. On May 5th the frigate struck upon the sand called "The Lemon and Oar," about sixteen leagues from the mouth of the Humber. This was caused by the carelessness of the pilot, to whom Pepys imputed "an obstinate over-weening in opposition to the contrary opinions of Sir I. Berry, his master, mates, Col. Legg, the Duke himself, and several others, concurring unanimously in not being yet clear of the sands." The Duke and his party escaped, but numbers were drowned in the sinking ship, and it is said that had the wreck occurred two hours earlier, and the accompanying yachts been at the distance they had previously been, not a soul would have escaped.
Pepys stayed in Edinburgh for a short time, and the Duke of York allowed him to be present at two councils. He then visited; with Colonel George Legge, some of the principal places in the neighbourhood, such as Stirling, Linlithgow, Hamilton, and Glasgow. The latter place he describes as "a very extraordinary town indeed for beauty and trade, much superior to any in Scotland."
Pepys had now been out of office for some time, but he was soon to have employment again. Tangier, which was acquired at the marriage of the King to Katharine of Braganza, had long been an incumbrance, and it was resolved at last to destroy the place. Colonel Legge (now Lord Dartmouth) was in August, 1683, constituted Captain-General of his Majesty's forces in Africa, and Governor of Tangier, and sent with a fleet of about twenty sail to demolish and blow up the works, destroy the harbour, and bring home the garrison. Pepys received the King's commands to accompany Lord Dartmouth on his expedition, but the latter's instructions were secret, and Pepys therefore did not know what had been decided upon. He saw quite enough, however, to form a strong opinion of the uselessness of the place to England. Lord Dartmouth carried out his instructions thoroughly, and on March 29th, 1684, he and his party (including Pepys) arrived in the English Channel.
The King himself now resumed the office of Lord High Admiral, and appointed Pepys Secretary of the Admiralty, with a salary of L500 per annum. In the Pepysian Library is the original patent, dated June 10th, 1684: "His Majesty's Letters Patent for ye erecting the office of Secretary of ye Admiralty of England, and creating Samuel Pepys, Esq., first Secretary therein." In this office the Diarist remained until the period of the Revolution, when his official career was concluded.
A very special honour was conferred upon Pepys in this year, when he was elected President of the Royal Society in succession to Sir Cyril Wyche, and he held the office for two years. Pepys had been admitted a fellow of the society on February 15th, 1664-65, and from Birch's "History" we find that in the following month he made a statement to the society:—
"Mr. Pepys gave an account of what information he had received from the Master of the Jersey ship which had been in company with Major Holmes in the Guinea voyage concerning the pendulum watches (March 15th, 1664-5)."
The records of the society show that he frequently made himself useful by obtaining such information as might be required in his department. After he retired from the presidency, he continued to entertain some of the most distinguished members of the society on Saturday evenings at his house in York Buildings. Evelyn expressed the strongest regret when it was necessary to discontinue these meetings on account of the infirmities of the host.
In 1685 Charles II. died, and was succeeded by James, Duke of York. From his intimate association with James it might have been supposed that a long period of official life was still before Pepys, but the new king's bigotry and incapacity soon made this a practical impossibility. At the coronation of James II. Pepys marched in the procession immediately behind the king's canopy, as one of the sixteen barons of the Cinque Ports.
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