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 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
Beagle was
commissioned on 4 July 1831 under his command, with Lieutenants
John Clements Wickham and
Bartholomew James Sulivan.
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 aft and forward. The
Cherokee-class ships had the reputation of being "
coffin" brigs, which handled badly and were prone to sinking. Apart from increasing headroom below, the raised deck made
Beagle less liable to top-heaviness and possible capsize in heavy weather by reducing the volume of water that could collect on top of the upper deck, trapped aboard by 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 the English scientist
William Snow Harris. FitzRoy spared no expense in her fitting out, which included
22 chronometers, 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. FitzRoy was influenced by the
physiognomy of
Lavater, and Darwin recounted in his autobiography that he was nearly "rejected, on account of the shape of my nose! He was an ardent disciple of Lavater, & was convinced that he could judge a man's character by the outline of his features; & he doubted whether anyone with my nose could possess sufficient energy & determination for 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.
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 combined this with details from his scientific notes 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 and a revised second edition, becoming known as
The Voyage of the Beagle. File:HMS Beagle by Conrad Martens.jpg|
Beagle being hailed by native Fuegians during the survey of
Tierra del Fuego, painted by
Conrad Martens who became ship's artist in 1833 File:HMS Beagle 1832 longitudinal section larger.jpg|Longitudinal section of HMS
Beagle as of 1832 File:TheBeagleLaidAshore.png|
The Beagle Laid Ashore by the
Santa Cruz river in Argentina, drawn by
Conrad Martens (1834), and engraved by
Thomas Landseer (1838) File:Admiralty Chart No 1375 Galapagos Islands, Published 1841.jpg|Admiralty Chart of the
Galápagos Islands, one of the charts resulting from Fitzroy's hydrographic surveys ==Third voyage (1837–1843)==