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:

"I would not omit giving you the knowledge of my having at last