On a difficult return voyage in 1788–1789 she became separated from her convoy and was found drifting helplessly off Rio de Janeiro with her crew incapacitated by scurvy.

After a period under French control, she returned to Britain and was used to carry trade goods between London, the West Indies and the Mediterranean.

[14] Both accounts give her initial owner as Cornhill merchant John Mather, who had previously purchased and disposed of Captain Cook's Endeavour after that vessel had returned from Botany Bay.

[15][16] A Lloyd's Register entry from 1787 also records that Mather owned a vessel named Hannibal, which had been renamed from Prince of Wales.

A second resupply took place in August in the Portuguese port of Rio de Janeiro, including the delivery aboard Prince of Wales of quantities of fresh fruit and vegetables, seeds, and some rum for the marines.

[22] Prince of Wales then turned southeast with the Fleet, reaching Cape Town in October and entering the Great Southern Ocean on 13 November for the last leg of the voyage to Australia.

[25] By mid-December the ship's supply of flour and butter for the voyage had been exhausted and Philip authorised Mason to broach the stores set aside for the future colony in order to continue to feed the convicts.

[27] Leaving Botany Bay she collided with Friendship, losing her mainmast staysail and topsail, but the damage was swiftly repaired and she was able to enter Port Jackson in line with her fellow transports.

[21] Convict health was comparatively good during the voyage, with a report by Governor Philip showing only nine cases of illness aboard Prince of Wales by the time she reached Tenerife, the least for any First Fleet transport.

[b] Indeed, Phillip wrote to Admiralty advising that "the convicts are not so sickly as when we sailed," though the women aboard Prince of Wales had no new clothing and were still in the ragged apparel they had worn in prison.

[30] As the Fleet headed toward Rio in July, humid conditions and heavy rains generated a "plague of bugs" below decks with more than a hundred insects found in one small sleeping area alone.

On 24 July the ship's longboat fell from a boom and struck 22-year-old Jane Bonner in the head; she died from her injuries six days later.

[33] The fact that Hartley was flogged, as punishment for the alleged planned mutiny, may have contributed to his poor health and subsequent death.

[35] The first recorded punishment of a convict aboard Prince of Wales was in October 1787, nearly nine months after she had sailed; six lashes for a woman caught stealing from her fellows while they were "at prayer.

[c] In October 1787 the wife of marine drummer Benjamin Cook died from an unspecified illness and was buried at sea after a brief ceremony.

[43] The plan was that the convoy sail north to rendezvous at Lord Howe Island, then set a course broadly parallel to the Great Barrier Reef with the aim of reaching the Dutch port of Batavia.

[43] This navigation plan was abandoned when both Prince of Wales and Borrowdale lost sight of Alexander and Friendship during a severe storm in late July, and found themselves alone and off course by the time the weather cleared.

The two lost ships anchored while their masters, John Mason in Prince of Wales and Hobson Reed in Borrowdale, consulted.

Instead, they agreed to turn their ships southeast into the open ocean and to return to England by sailing the other way around the world, via Cape Horn and Rio de Janeiro and then northeast across the Atlantic to Europe.

[45] Throughout the voyage her crew had been heavily reliant on a diet of salted meat and by early September scurvy had incapacitated the majority.

She drifted helplessly in the outer harbor until Rio's harbourmaster sighted her the following morning and had additional seamen rowed out to assist.

A resupplied Prince of Wales set sail from Rio on Christmas Day 1788, completing an uneventful final leg to reach Falmouth in England on 25 March 1789.

Despite the delays of disease, weather and an unfamiliar route, she was the first of the Fleet to return home, two months ahead of Alexander which did not reach England until 28 May.

Prince of Wales departed on a cruise and on 7 April she captured the French merchant vessel "Le Federatis", which was sailing from Cap-François to Bordeaux with a cargo valued at £40,000,[49] or £32,000.

[e] Plans changed, and Tarleton appointed Captain James Thomson (or Thompson) to command of Prince of Wales, with the intent of sailing her on the Liverpool-Africa trade, i.e., as a slaver.

Lastly, in early 1974, Prince of Wales captured and brought in Flugen, of Malmö, which had been carrying wine, brandy, and bale goods from Bordeaux to Saint-Domingue.

[62] The process by which she returned to British ownership is currently obscure, but one suspects that the Royal Navy recaptured her in the West Indies, but so far evidence for the conjecture is lacking.