"Indefatigable" was under the command of Commander George Andrews. On 12 July "Indefatigable" departed Spithead for Hull. She returned to the Downs from Hull on 29 August. The Navy returned the armed defence ships to their owners in late 1804 or in 1805. Next, "Indefatigable" was one of the transport vessels that were part of the expedition under General Sir David Baird and Admiral Sir Home Riggs Popham that would in 1806 capture the Dutch Cape Colony. On 21 March 1806 she sailed with 16 other transports in a convoy to Great Britain with invalids and Dutch prisoners. The newly-captured and commissioned HMS "Volontaire" provided their escort. "Indefatigable" was under charter to the EIC and under the command of John Cross, when she left England on 4 June 1812, passing the Lizard on 7 June. She sailed together with and they reached Rio de Janeiro on 29 July. There they joined the "Archduke Charles", which was transporting convicts from Ireland, also for Port Jackson. The three vessels left Rio together on 11 August, but "Archduke Charles" parted the next day. Six days after they left Rio, a gale separated "Minstrel" and "Indefatigable". She arrived at Hobart Town on 19 October. "Indefatigable" had left with 200 convicts and she landed 199, one having died on the way. "Indefatigable" left Hobart Town and arrived at Port Jackson on 6 December. She left Port Jackson on 7 January 1813 bound for England. She arrived at the Cape on 6 August, "Indefatigable" had been at Canton, where she had loaded a modest cargo of tea and no textiles. From the Cape she sailed to St Helena, where she arrived on 5 September. She apparently did not leave St Helena until 1 March 1814, but then reached Blackwall on 19 May. On her second convict voyage, under the command of Matthew Bowles, "Indefatigable" left England in 1814. She sailed via Rio de Janeiro and arrived at Port Jackson on 26 April. She transported 200 male convicts, two of whom died on the voyage. "Indefatigable" left Port Jackson on 13 July bound for Bengal. While anchored at Batavia (now Jakarta), "Indefatigable" was burnt to the waterline in an accident on 23 October 1815 and declared a total loss.