flagship of Rear-admiral Peter Rainier [q. v.], by whom he was promoted, on 13 Jan. 1798, to be lieutenant of the Victorious of 74 guns, then commanded by Captain William Clark. On 30 June Clark suspended him from duty and placed him under arrest for disrespectful behaviour. Afterwards he remitted the punishment and ordered him to return to his duty. This Willoughby declined to do without an acknowledgment that the arrest was unjust; and as Clark refused this, he applied for a court-martial. It was nearly twelve months before a court could be assembled, and Willoughby was then convicted of having ‘behaved to Captain Clark in a contemptuous and disrespectful manner;’ but, in consideration of his long confinement, only sentenced ‘to be dismissed his ship.’ Rainier, thinking probably that twelve months' confinement in the tropics had fully punished him, appointed him the next day, 14 June 1799, to command the Amboyna brig; but the imprisonment had told severely on Willoughby's health, and he was obliged to invalid, taking a passage in the Sceptre for the Cape of Good Hope. On the way thither he piloted the ship's boat through a reef of rocks at Rodriguez, and captured a French privateer brig which had sought safety within it. On 5 Nov. the Sceptre was blown from her anchor and driven on shore in Table Bay, with the loss of her captain and a great part of her crew. Willoughby, with many of the officers, was at a ball on shore, and so escaped.
In August 1800 he was appointed to the Russell, one of the fleet which went to the Baltic in the following spring, and of the squadron which, under the command of Nelson, fought the battle of Copenhagen on 2 April. In this, Willoughby's conduct in boarding under a heavy fire and taking possession of the Danish ship Provesteen was highly commended; and as he returned to his ship on the next day he was loudly cheered by his shipmates, on the order of the captain. But the captain was not a pleasant man to work with, and Willoughby repaid his overbearing conduct with studied insolence. Each applied for a court-martial on the other. The captain was tried for tyranny and oppression on 22 June, and was, notwithstanding the evidence, acquitted, the charges being pronounced ‘frivolous, scandalous, malicious, and totally unfounded, tending to lessen the dignity and to subvert the good order and discipline of his majesty's naval service.’ The next day Willoughby in turn was tried ‘for treating his captain with insolence and contempt,’ and, as this was proved by the evidence, he was dismissed the service; his previous trial for a similar offence and the judgment of the court on the previous day certainly telling against him (Courts Martial, vol. xcvi.)
On the renewal of the war in 1803 Sir John Thomas Duckworth [q. v.], then going out to the West Indies as commander-in-chief, received Willoughby on board his flagship as a volunteer; and on his report the sentence was remitted and Willoughby repromoted to be lieutenant on 26 Oct. 1803. In November Duckworth's flagship, the Hercule, to which Willoughby belonged, was sent to join the squadron under Commodore Loring, then blockading Cape Français, in co-operation with the revolted negroes under General Dessalines. By the end of the month the garrison had concluded a treaty with Dessalines, by which they were to embark on board their ships in the port and put to sea on or before the 30th. But as Loring would not accept anything but absolute surrender, and they could not elude his vigilance, they were obliged to capitulate. The ships were to come out of the harbour with their colours flying, fire a complimentary broadside, and strike their flags. M. Montalan, commanding the French frigate Clorinde, is described as refusing to accept this convention, and attempting to escape (Troude, iii. 300). In doing this his ship took the ground under the negro batteries, which were preparing to set her on fire with red-hot shot, or, as an alternative, put to death every soul that landed from her. Willoughby, who was in command of the Hercule's launch—one of the boats which had been towing the other ships out of the mole—seeing the Clorinde's imminent danger, went on board her, persuaded Montalan and the officer commanding the troops to surrender at once, hoisted the English flag, and eventually succeeded in bringing the ship off, to be added to the English navy. The preservation of nine hundred lives was thus owing, Duckworth wrote, to Willoughby's uncommon exertions and professional ability (James, iii. 206; cf. Travers, Sir Eaton Standard). Marshall thinks that it was for his conduct on this occasion that Willoughby was restored to his rank; but if so, the commission would have been dated 30 Nov.; it was, in fact, more than a month earlier, though he had not yet had the news of it.
In the operations against Curaçoa, in February 1804, Willoughby was in command of an advanced battery, exposed to the frequent assaults of vastly superior numbers, in repelling which and by sickness his little force was almost exterminated.
