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he obtained leave from the admiralty, and went to Ostend, whence he sailed for India in command of a merchant ship under the imperial flag. At Calcutta he was favourably received by Lord Cornwallis, at whose request he made a survey of New Harbour in the Hooghley, with a view to the establishment of a dockyard. Having returned to Ostend, he made a second voyage in 1790, with a cargo belonging wholly or in great part to an English house at Ostend. At Calcutta he undertook to carry a cargo of rice to the Malabar coast for the use of the company's army, but was driven to the eastward by the strength of the monsoon, and forced to bear up for Pulo Penang. There, while the ship was refitting, he made an exact survey of the island, and discovered a new channel to the southward, through which, in the spring of 1792, he piloted the company's fleet to China. For this piece of work he was presented with a gold cup by the governor-general in council, who also wrote very strongly in his favour to the court of directors, requesting them to represent Popham's services to the admiralty ‘in the terms they merit.’ He was at this time on terms of intimacy with the deputy-governor and several members of the council; and with their knowledge in December 1791 he purchased and fitted out, at a cost of about 20,000l., an American ship, the President Washington, whose name he changed to Etrusco. In her he went to China, took on board a cargo to the value of near 50,000l., the joint property of himself and two merchants, apparently French, the freight of which, to the amount of 40,000l., was entirely his own. On arriving at Ostend in July 1793 the Etrusco was seized by the English frigate Brilliant, brought into the Thames, claimed as a prize for having French property on board, and condemned as a droit of admiralty, apparently for illegal trading in contravention of the charter of the English East India Company. Popham's contention was virtually that he had rendered important services to the company, and that his voyage was sanctioned by the governor-general in council. The case was the subject of prolonged litigation. It was not till 1805 that Popham received a grant of 25,000l. as a compensation for the loss of about 70,000l., the value of his stake in the Etrusco, not including the heavy costs of the lawsuit (Parl. Papers, 1808, vol. x.; Parl. Hist. 11 Feb. 1808; Nav. Chron. xix. 151, 312, 406; Edin. Rev. May 1820, pp. 482–3).

Meantime, and immediately on his return to England in 1793, Popham, under the immediate orders of Captain Thompson, was attached to the army in Flanders under the Duke of York, who on 27 July 1794 forwarded to the admiralty a strong commendation of the conduct and services of Popham as superintendent of the inland navigation. ‘His unremitting zeal and active talents have been successfully exerted in saving much public property on the leaving of Tournay, Ghent, and Antwerp.’ He therefore requested that Popham might ‘be promoted in the line of his profession, and still be continued in his present employment, where his service is essentially necessary’ (Nav. Chron. xix. 407). The recommendation was not attended to till after a second letter from his royal highness, when the commission as commander was dated 26 Nov. 1794. When the campaign was ended the duke wrote again, on 19 March 1795, and this time personally to the first lord of the admiralty, commending Popham's exertions, and concluding with a request that he might ‘be promoted to the rank of post captain.’ This was accordingly done on 4 April 1795.

In the years immediately following Popham drew up a plan for the establishment and organisation of the sea-fencibles, and in 1798 he was appointed to command the district from Deal to Beachy Head. In May he had command of the naval part of the expedition to Ostend to destroy the sluices of the Bruges Canal [see Coote, Sir Eyre, (1762–1824?)], and in 1799 was sent to Cronstadt in the Nile lugger to make arrangements for the embarkation of a body of Russian troops for service in Holland. The emperor, with the empress and court, visited him on board the lugger, presented him with a gold snuff-box set with diamonds, and constituted him a knight of Malta, an honour which was afterwards sanctioned by his own sovereign. The empress, too, gave him a diamond ring. After inspecting several of the Russian ports and making the necessary arrangements, Popham returned to England. In the following winter he had command of a small squadron of gunboats on the Alkmaar Canal, and was able to render efficient support to the army in its first encounter with the enemy. The expedition, however, ended in disaster, and the troops returned ingloriously. Popham's services were rewarded with a pension of 500l. a year.

In 1800 he was appointed to the Romney of 50 guns, in command of a small squadron ordered to convoy troops from the Cape of Good Hope and from India up the Red Sea, to co-operate with the army in Egypt under Sir Ralph Abercromby, and to conclude a commercial treaty with the Arabs in the neighbourhood of Jeddah. When this had