though he was ‘mightily pleased’ by her consenting to go to church with him (29 Nov. and 6 Dec. 1668). Probably she had received some impressions from her life in the convent, although Pepys obtained afterwards a letter from her brother denying that she had ‘the least thoughts of popery’ (Smith, i. 147). The Duke of York was endeavouring at this time to obtain Pepys's election to a seat vacated at Aldborough, Suffolk, by the death of Sir Robert Brooke. Pepys was prevented by his wife's last illness from attending at the election; and, in spite of the influence of the duke and Lord Henry Howard (afterwards sixth Duke of Norfolk), the choice fell upon John Bruce. In November 1670 Pepys was nearly fighting a duel with the Swedish resident, Leyenbergh, who, in 1671, married the widow of Sir William Batten [q. v.], one of Pepys's colleagues. Batten owed him money, and the quarrel, as Lord Braybrooke suggests, may have arisen in some way out of this. The meeting, however, was stopped by the king's orders.
Pepys's patron, Montagu, who had become first Earl of Sandwich, was killed in action on 28 May 1672. Pepys had been a serviceable client; he had remonstrated very sensibly with Lord Sandwich for neglecting his duties in consequence of a connection with a mistress (9 Sept. and 18 Nov. 1663), and in 1665 he was employed in bringing about the marriage between Sandwich's daughter, Lady Jemima, and Philip, son of the treasurer of the navy, Sir George Carteret [q. v.] Pepys, however, was now independent. In the summer of 1673 the Duke of York resigned his posts upon the passage of the Test Act. The admiralty was thereupon put into commission, and Pepys was appointed, about June 1673, ‘secretary for the affairs of the navy.’ He obtained the appointment to his old office of his clerk, Thomas Hayter, and his brother, John Pepys. John had been at St. Paul's School, and was scholar of Christ's College, Cambridge, and in 1670 Pepys had obtained his appointment to be clerk of the Trinity House. He died unmarried in 1677, owing 300l. to the Trinity House, which Pepys had to pay. The elevation to the peerage of Sir Robert Paxton caused a vacancy for Castle Rising. The Duke of York had, in 1672, obtained a promise from Howard to support Pepys. As Howard had given other promises to the king and the Duchess of Cleveland there was some difficulty; but Pepys was ultimately elected on 4 Nov. 1673. On a petition from his opponent the election was pronounced to be void by the committee of privileges, but as the house did not come to a vote he was permitted to retain his seat. He was afterwards accused of having an altar with a crucifix in his house, and being ‘a papist and popishly inclined.’ Pepys appears to have had either a crucifix or a picture of the crucifixion (Diary, 20 July, 2 Aug., 3 Nov. 1666), but he entirely denied the charge. It rested upon vague statements by Lord Shaftesbury and Sir John Banks; but as Shaftesbury could remember nothing distinctly, and Banks denied having said anything, the charge was dropped. In 1676 Pepys was master of the Trinity House and in 1677 master of the Clothworkers' Company, to whom he presented a silver cup, still preserved. He appears from a reference in the debates (Parl. Hist. iv. 976–6) to have been regarded as assuming dictatorial authority in naval matters. In February 1678–9 Pepys was receiving applications from Portsmouth, the Isle of Wight boroughs, and Harwich to become member. He chose to stand for Harwich, and sat as its representative in the Short parliament of 1679. He was now the object of an attack which was made dangerous by the excitement of the ‘popish plot’ (‘Pepys and the Popish Plots,’ Hist. Rev. p. 492). His intimacy with the Duke of York was likely to rouse suspicions. His clerk, Samuel Atkins, had been accused of being accessory to the murder of Sir Edmund Berry Godfrey [q. v.], but was acquitted on 8 Feb. 1678–9. Atkins had been employed by the Duke of York to collect evidence against one John Scott, who was proved guilty of fraud. Scott now accused Pepys and his colleague, Sir Anthony Deane, of sending in 1675 information about the navy to the French government, and of conspiring to extirpate the protestant religion. They were committed to the Tower under the speaker's warrant on 22 May 1679, and Hayter succeeded to Pepys's office at the admiralty. Pepys was put to great expense in preparing a defence. He had to employ his brother-in-law, St. Michel, to collect evidence. A music-master, Morelli, who had lived with him, was supposed to be a priest in disguise, and Pepys had to appeal to him to disprove the report (Smith, i. 192, 198). The trial was postponed several times, though the prisoners were ultimately allowed to find security for 30,000l. At length, on 12 Feb. 1679–80, they applied for a discharge, when the attorney-general consented, Scott having refused to support his original deposition. John James, who had been a butler to Pepys, died in March 1680, and confessed that he had trumped up the charge (ib. i. 216, 271). William Harbord, M.P. for Thetford, was an enemy of Pepys, and, according to his belief,
