Fitzroy had been given reason to hope that the South American Survey would be continued under his command, but when the Lords of the Admiralty appeared to abandon the plan, he made alternative arrangements to return the Fuegians. A kind uncle heard of this and contacted the Admiralty. Soon afterwards Fitzroy heard that he was to be appointed commander of HMS Chanticleer to go to Tierra del Fuego, but due to her poor condition Beagle was substituted for the voyage. Fitzroy was re-appointed as commander on 27 June 1831 and the Beagle was commissioned on 4 July 1831 under his command, with Lieutenants John Clements Wickham and Bartholomew James Sulivan.
Longitudinal section of HMS Beagle as of 1832
Beagle was immediately taken into dock at Devonport for extensive rebuilding and refitting. As she required a new deck, Fitzroy had the upper-deck raised considerably, by 8 inches (200 mm) aft and 12 inches (300 mm) forward. The Cherokee-class ships had the reputation of being “coffin” brigs, which handled badly and were prone to sinking; the raised deck gave the Beagle better handling and made her less liable to become top-heavy and capsize by helping the decks to drain more quickly so that less water would collect in the gunwales. Additional sheathing added to the hull added about seven tons to her burthen and perhaps fifteen to her displacement.
The ship was one of the first to be fitted with the lightning conductor invented by William Snow Harris. Fitzroy spared no expense in her fitting out, which included 22 chronometers, and five examples of the Sympiesometer, a kind of mercury-free barometer patented by Alexander Adie which was favoured by Fitzroy as giving the accurate readings required by the Admiralty. To reduce magnetic interference with the navigational instruments, Fitzroy proposed replacing the iron guns with brass guns, but the Admiralty turned this request down. (When the ship reached Rio de Janeiro in April 1832, he used his own funds for replacements: the ship now had a “six-pound boat-carronade” on a turntable on the forecastle, two brass six-pound guns before the main-mast, and aft of it another four brass guns; two of these were nine-pound, and the other two six-pound.)
Fitzroy had found a need for expert advice on geology during the first voyage, and had resolved that if on a similar expedition, he would “endeavour to carry out a person qualified to examine the land; while the officers, and myself, would attend to hydrography.” Command in that era could involve stress and loneliness, as shown by the suicide of Captain Stokes, and Fitzroy’s own uncle Viscount Castlereagh had committed suicide under stress of overwork. His attempts to get a friend to accompany him fell through, and he asked his friend and superior, Captain Francis Beaufort, to seek a gentleman naturalist as a self-financing passenger who would give him company during the voyage. A sequence of inquiries led to Charles Darwin, a young gentleman on his way to becoming a rural clergyman, joining the voyage.
Beagle was originally scheduled to leave on 24 October 1831 but because of delays in her preparations the departure was delayed until December. Setting forth on what was to become a ground-breaking scientific expedition she departed from Devonport on 10 December. Due to bad weather her first stop was just a few miles ahead, at Barn Pool, on the west side of Plymouth Sound,. The Beagle left anchorage from Barn Pool on 27 December, passing the nearby town of Plymouth. After completing extensive surveys in South America she returned via New Zealand, Sydney, Hobart Town (6 February 1836), to Falmouth, Cornwall, England on 2 October 1836.
Darwin had kept a diary of his experiences, and rewrote this as the book titled Journal and Remarks, published in 1839 as the third volume of the official account of the expedition. This travelogue and scientific journal was widely popular, and was reprinted many times with various titles, becoming known as The Voyage of the Beagle. This diary is where Darwin drew most of the ideas for his publications. Darwin attributes his first real training in natural history to his voyage on the Beagle.