Parker (1739–1807) [q. v.] to be chaplain of his flagship, the St. George. Parker conceived a warm friendship for him, and employed him as a foreign secretary.
Subsequently Scott accompanied Parker to the West Indies in the Queen. At Jamaica, by Parker's interest with the governor, he was appointed to a living in the island, of the value of 500l. a year, tenable with his chaplaincy. In 1800 Parker returned to England, and Scott went with him on leave of absence, joining him in the London when he hoisted his flag as commander-in-chief of the fleet going to the Baltic. With his remarkable aptitude for languages, Scott, who already had a good knowledge of German, quickly picked up Danish, and was at work on Russian. After the battle of Copenhagen he was employed as secretary to the conferences on shore, Nelson, who had known him in the Mediterranean, making a special request to Parker for his assistance. Afterwards, when Parker was recalled, he refused Nelson's invitation to come to the St. George, saying that ‘he could not bear to leave the old admiral at the very time when he stood most in need of his company.’ Nelson made him promise that he would come to him when he could leave Sir Hyde.
In the last days of 1801 he learned that his living in Jamaica would be declared vacant if he did not return at once. He accordingly went out in the Téméraire, and arrived at Port Royal on 5 April 1802, when he was appointed by Sir John Thomas Duckworth [q. v.] to be chaplain of the flagship, the Leviathan, and despatched on a secret message to Cape Français, to try and ascertain the intention of the French in sending an army of twenty thousand men to St. Domingo after peace had been concluded. He failed to solve that puzzle, but found that sickness had so disorganised the French ranks that nothing was to be apprehended from them. While returning to the admiral in the frigate Topaze the ship was struck by lightning, and he was seriously injured. To physical trouble was added the worry of finding, on arrival at Kingston, that his living had been given away by the governor. Meantime, however, the governors of the Charterhouse had presented him to the vicarage of Southminster in Essex, which he visited early in 1803, after his passage home. Nelson, who visited him while both were stopping in London, persuaded Scott to go out with him when appointed to the Mediterranean command in May 1803. He sailed in the Amphion, from which he was transferred, off Toulon, to the Victory. As private secretary and interpreter he was able to render Nelson efficient assistance in a private capacity. Officially, he was chaplain of the Victory, and nothing else. The arrangement by which Nelson paid him 100l. a year was entirely a private one. He was frequently sent, as though on leave, to Leghorn, Naples, Barcelona, or other places; and the readiness with which he gained admission to fashionable society enabled him to bring back important intelligence, or occasionally to obtain concessions which would certainly not have been granted on formal application. He continued with Nelson on this footing for the whole time in the Mediterranean, during the chase to the West Indies, and till he landed at Portsmouth on 20 Aug. 1805. Before the end of the month he again joined Nelson at Merton, and on 15 Sept. sailed with him once more in the Victory. On 21 Oct. he attended during the dying admiral's last hours, receiving his last wishes. On the return of the Victory to England he attended the coffin as it lay in state at Greenwich, and till it was finally laid in the crypt of St. Paul's.
The only public recognition Scott received for his services was the degree of D.D. conferred on him by Cambridge on the royal mandate. The admiralty refused to acknowledge his unofficial services, and even stopped his time and pay as chaplain for the many weeks he had been absent from his ship on leave. This was strictly in conformity with established usage, though the stoppage was eventually withdrawn.
Scott settled down as vicar of Southminster on a narrow income, scantily extended by a small half pay. In 1816 Lord Liverpool presented him to the crown living of Catterick in Yorkshire, and at the same time he was appointed chaplain to the prince regent, which gave him the right of holding two livings. From this time he lived principally at Catterick, engaged in the duties of his profession and accumulating a large library, mostly of foreign books. Among them were represented forty different languages, of many of which, however, his knowledge was very limited. He died at Catterick on 24 July 1840, and was buried in the churchyard of Ecclesfield, near Sheffield, on the 31st. In July 1807 he married Mary Frances, daughter of Thomas Ryder, registrar of the Charterhouse. She died in September 1811, leaving two daughters, the younger of whom, Margaret, wife of Dr. Alfred Gatty [q. v.], vicar of Ecclesfield, is separately noticed [see Gatty].
[Recollections of the Life of the Rev. A. J. Scott (by his daughter and son-in-law, Mrs. and Dr. Gatty), mainly made up of Scott's letters
