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: