It appears from the endorsement of a letter from Balthasar St. Michel to Pepys, to which allusion has already been made, that the latter was actually charged with having turned Mrs. Pepys from a Protestant to a Roman Catholic. Pepys therefore obtained from her brother an account of the fortunes of their family, which shows the utter absurdity of any such imputations.[87] He was always a true Protestant, although there is some reason for believing that Mrs. Pepys was a Catholic at heart.[88] On the passing of the Test Act, in 1673, the Duke of York resigned all his employments; and the Admiralty being put in commission, Pepys, as secretary, was brought in immediate correspondence with Charles II.
In 1677[89] he was elected Master of the Clothworkers’ Company, when he presented a richly-chased silver cup, which is still used at their dinners. He was not long allowed to remain in peace, for the charge of popery, which was first made in 1673, was frequently repeated, and in 1679 he was accused, on the depositions of Colonel John Scott, of betraying the navy, by sending secret particulars to the French Government; and also of a design to dethrone the King and extirpate the Protestant religion. He and Sir Anthony Deane were committed to the Tower under the Speaker’s warrant on May 22nd, and Pepys’s place at the Admiralty was filled up 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 _£_30,000. At length, after several months of delay, it was found that Colonel Scott refused to acknowledge to the truth of the original deposition; and the prisoners were relieved from their bail on February 12th, 1679–80. Scott turned out to be a blackguard. He is said to have cheated the States of Holland out of _£_7,000, in consequence of which he was hanged in effigy at the Hague, in 1672; and in 1681 he fled from England to escape from the law, as he had been found guilty of wilful murder for killing a coachman. 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. Harbord, M.P. for Launceston, a leading enemy of Pepys.[90]