In July 1802 he joined Centaur under Captain Bendall Robert Littlehales, and after taking part in the capture of Saint Lucia under Admiral Sir Samuel Hood, he and Littlehales returned home aboard the hired brig Morne Fortunee with despatches in June 1803. He was then attached to Northumberland, Captain the Honourable Alexander Cochrane, but soon returned to the West Indies to serve aboard Theseus under Captain John Bligh in operations at Saint-Domingue. Baker took part in the blockade of Cape François; the capture of Fort Dauphin, where two forts and a 28-gun corvette La Sagesse, were taken; and the surrender of the French squadron with the remains of General Rochambeau's army on board.[4]
On 16 July 1804 Baker followed Captain Bligh into the frigate Surveillante with the rank of acting-lieutenant. In March 1805 he was transferred 18-gun Reynard under the command of Captain Jeremiah Coghlan. On 20 March the Reynard destroyed a large French privateer General Ernouf, as a result of which Baker's commission was confirmed and backdated to 18 October 1804. In December 1805 he joined the Fortunée under Captain Henry Vansittart, then from May 1806 served aboard Mediator under Captain William Furlong Wise as first lieutenant. He took part in the capture of several privateers, and the storming of the fort at Samaná on 14 February 1807. He then served aboard Veteran, the flagship of Rear-Admiral James Richard Dacres.[4]
Baker returned home in late 1807 and joined the Castor under Captain William Roberts, then Eagle under Captain Rowley again, and Leda under George Sayer. In August 1809, he took charge of a gun-boat, and was particularly mentioned by Sir George Cockburn for his part at the bombardment of Vlissingen during the Walcheren Campaign. On 15 August 1810, he assumed command of a 10-gun schooner named Anholt, and served as second in command under Captain James Wilkes Maurice at the defence of Anholt, in March 1811 when that island was attacked by a Danish force at least four times larger than the British garrison. Baker in Anholt played a major part in the defeat of the enemy by bearing down along the northern shore of the island, and placing them between two fires. This was acknowledged, on his arrival in England with despatches, by promotion to the rank of commander dated 8 April 1811.[4]
On 27 June 1820 he married Louisa Ann Williams, the daughter of William Williams of Belmont House, South Lambeth, formerly MP for Weymouth,[4] and had two sons and five daughters.[5] He succeeded his father as second baronet on 4 February 1826.[4]
On 29 July 1840, Baker was selected by Vice-Admiral Sir Henry Digby, Commander-in-Chief, The Nore, to be his flag captain in the Howe at Sheerness. In October 1841, a few days after transferring with Digby to Camperdown, while in attendance on the Lords of the Admiralty, he unfortunately broke his leg and received other severe injuries. He resigned the command of Camperdown in December, and on 19 January 1842 was granted a pension of £180.[4] He was promoted to rear-admiral on 6 November 1850, and to vice-admiral on 9 July 1857.[1] Vice-Admiral Baker died on 2 November 1859.[4]