When Pepys ceased to be Clerk of the Acts he was able to obtain the appointment for his clerk, Thomas Hayter, and his brother, John Pepys, who held it jointly. The latter does not appear to have done much credit to Samuel. He was appointed Clerk to the Trinity House in 1670 on his brother’s recommendation, and when he died in 1677 he was in debt L300 to his employers, and this sum Samuel had to pay. In 1676 Pepys was Master of the Trinity House, and in the following year Master of the Clothworkers’ Company, when he presented a richly-chased silver cup, which is still used at the banquets of the company. On Tuesday, 10th September, 1677, the Feast of the Hon. Artillery Company was held at Merchant Taylors’ Hall, when the Duke of York, the Duke of Somerset, the Lord Chancellor, and other distinguished persons were present. On this occasion Viscount Newport, Sir Joseph Williamson, and Samuel Pepys officiated as stewards.
About this time it is evident that the secretary carried himself with some haughtiness as a ruler of the navy, and that this was resented by some. An amusing instance will be found in the Parliamentary Debates. On May 11th, 1678, the King’s verbal message to quicken the supply was brought in by Mr. Secretary Williamson, when Pepys spoke to this effect:
“When I promised that the ships should be ready by the 30th of May,
it was upon the supposition of the money for 90 ships proposed by
the King and voted by you, their sizes and rates, and I doubt not by
that time to have 90 ships, and if they fall short it will be only
from the failing of the Streights ships coming home and those but
two.....
“Sir Robert Howard then rose and said, ‘Pepys here speaks rather
like an Admiral than a Secretary, “I” and “we.” I wish he knows
half as much of the Navy as he pretends.’”
Pepys was chosen by the electors of Harwich as their member in the short Parliament that sat from March to July, 1679, his colleague being Sir Anthony Deane, but both members were sent to the Tower in May on a baseless charge, and they were superseded in the next Parliament that met on the 17th October, 1679.
The high-handed treatment which Pepys underwent at this time exhibits a marked instance of the disgraceful persecution connected with the so-called Popish plot. He was totally unconnected with the Roman Catholic party, but his association with the Duke of York was sufficient to mark him as a prey for the men who initiated this “Terror” of the seventeenth century. Sir. Edmund Berry Godfrey came to his death in October, 1678, and in December Samuel Atkins, Pepys’s clerk, was brought to trial as an accessory to his murder. Shaftesbury and the others not having succeeded in getting at Pepys through his clerk, soon afterwards attacked him more directly, using the infamous evidence of Colonel Scott. Much light has lately been thrown upon the underhand dealings of this miscreant by Mr. G. D. Scull, who printed privately in 1883 a valuable work entitled, “Dorothea Scott, otherwise Gotherson, and Hogben of Egerton House, Kent, 1611-1680.”
John Scott (calling himself Colonel Scott) ingratiated himself into acquaintance with Major Gotherson, and sold to the latter large tracts of land in Long Island, to which he had no right whatever. Dorothea Gotherson, after her husband’s death, took steps to ascertain the exact state of her property, and obtained the assistance of Colonel Francis Lovelace, Governor of New York. Scott’s fraud was discovered, and a petition for redress was presented to the King. The result of this was that the Duke of York commanded Pepys to collect evidence against Scott, and he accordingly brought together a great number of depositions and information as to his dishonest proceedings in New England, Long Island, Barbadoes, France, Holland, and England, and these papers are preserved among the Rawlinson Manuscripts in the Bodleian. Scott had his revenge, and accused Pepys of betraying the Navy by sending secret particulars to the French Government, and of a design to dethrone the king and extirpate the Protestant religion. Pepys and Sir Anthony Deane were committed to the Tower under the Speaker’s warrant on May 22nd, 1679, and Pepys’s place at the Admiralty was filled by the appointment of Thomas Hayter. When the two prisoners were brought to the bar of the King’s Bench on the 2nd of June, the Attorney-General refused bail, but subsequently they were allowed to find security for L30,000.
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:—
“His Majesty of his gracious regard to me, and the justification of
my innocence, was then pleased at my humble request to dispence with
my said brother goeing (with ye shippe about that time designed for
Tangier) and to give leave to his goeing into France (the scene of
ye villannys then in practice against me), he being the only person
whom (from his relation to me, together with his knowledge in the
place and language, his knowne dilligence and particular affection
towards mee) I could at that tyme and in soe greate a cause pitch
on, for committing the care of this affaire of detecting the
practice of my enemies there.”
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: