This mission occupied most of the year, Thompson organising the government of the colonies and taking measures for their defence. Rodney had returned to England; Sir Samuel Hood, left in command, had gone to New York; and in November, Thompson, at the request of merchants, convoyed their trade to Barbados. He took on himself the responsibility of shipping it to Europe. In his absence, the Guiana colonies were captured by a small French squadron; and on 1 April Thompson was tried by court-martial on the charge of having left his station and returned to England without orders. The court, however, honourably acquitted him. In 1782 he was appointed to the 50-gun , in which he went out to the west coast of Africa as commodore of the small squadron there. He died, unmarried, on board the "Grampus" on 17 January 1786. His portrait was engraved by A. McKenzie. His anonymous satire "The Meretriciad" (1755?), in which he celebrated the charms of Kitty Fisher and some of her associates, reached a sixth edition in 1765. It was followed by the ‘Demi-Rep’ (1756), by the ‘Courtesan,’ and by several other ‘Meretricious Miscellanies,’ as the author called them. None of these works bore the author's name. They were collected in 1770 under the collective title of "The Court of Cupid". In the previous year he had issued a boisterous ode entitled ‘Trinculo's Trip to the [Stratford] Jubilee.’ It was dedicated to ‘John Hall’, i.e. John Hall Stevenson. His ‘Sailor's Letters, written to his Select Friends in England during his Voyages and Travels in Europe, Asia, Africa, and America, from the year 1754 to 1759’ (2 vols. 1767), which depicts the social life of the navy, as well as giving an account of the battle of Quiberon Bay. Thompson also edited the "Works" of John Oldham (3 vols. 1771); of Andrew Marvell (3 vols. 1776); and of Paul Whitehead (1777). He wrote sea songs including ‘Loose every Sail to the Breeze,’ and ‘The Topsail shivers in the Wind.’ In 1773 he altered from the old play of Charles Shadwell ‘The Fair Quaker: or the Humours of the Navy,’ which was produced at Drury Lane on 11 November 1773 and then printed.