great measure rested upon Pepys alone. He behaved with calm and
deliberate courage and integrity. Nevertheless, he had the
misfortune to experience some part of the calumnies of the time
of "the Popish Plot." The Earl of Shaftesbury, the foster-father
of this most wicked delusion, showed a great desire to implicate
Pepys in a charge of Catholicism, and went so far as to spread a
report that the Clerk of the Acts had in his house an altar and a
crucifix. The absence not only of evidence, but even of ground
of suspicion, did not prevent Pepys being committed to the Tower
on the charge of being an aider and abettor of the plot, and he
was, for a time, removed from the Navy Board. He was afterwards
allowed, with Sir Anthony Deane, who had been committed with him,
to find security in 30,000l.; and upon the withdrawal of the
deposition against him, he was discharged. He was soon, by the
special command of Charles II., replaced in a situation where his
skill and experience could not be well dispensed with; and rose
afterwards to be Secretary of the Admiralty, which office he
retained till the Revolution. It is remarkable that James II.
was sitting to Sir Godfrey Kneller for a portrait designed as a
present to Pepys, when the news of the landing of the Prince of
Orange was brought to that unhappy monarch. The King commanded
the painter to proceed, and finish the portrait, that his good
friend might not be disappointed.

Pepys had been too much personally connected with the King, (who
had been so long at the Admiralty,) to retain his situation upon
the accession of William and Mary; and he retired into private
life' accordingly, but without being followed thither, either by
persecution or ill will.