On 14 June 1799, Rainier appointed Lieutenant William Josiah Willougby to command Amboyna. Willoughby had been a midshipman on Suffolk at the capture of Ambon and Banda, and just emerged from a year under arrest. He had demanded a court-martial after Captain William Clark of , on which he was then serving, had arrested him for "disrespectful behaviour" and then withdrawn the charge. The court martial found Willougby guilty but had sentenced him to time served and ordered him reinstated to his rank; the court martial also exonerated Clark. Willoughby declined the appointment due to ill-health brought on by his confinement and returned to England.'"Dictionary of National Biography", (1900), Vol. 62 (Williamson-Worden), pp. 37-8.
