Please note that images or descriptions below might contain spoilers, as in paintings that represent events in the novels or pictures from the film.
"... she was a slow brig, an old brig and a brig that was very unlikely to make his fortune."
1800 - 1801: Jack Aubrey's first command, described in Master and Commander, is the brig-rigged "sloop" HMS Sophie, operating out of Port Mahon in the western Mediterranean. Towards the end of the novel, the first book in the series, Sophie is captured on the Spanish coast by a French squadron led by Admiral Linois.
Although the activities of the Sophie and her dimensions and armament were modeled closely on those of real-life HMS Speedy, commanded by Thomas, Lord Cochrane, the quarterdeck - unusual for a small sloop - was taken from HMS Vincejo, captured from the Spanish navy in 1799. Indeed, In the novel the Sophie is pointed out by one naval officer as being the former "Vencejo" - an alternative spelling - although in fact the Vincejo kept its original name while serving in the Royal Navy until captured by the French at Quiberon Bay in 1804. The Speedy, like the fictional Sophie, was captured in 1801 by Linois.
"She was known as the Carpenter's Mistake, and no one in the service had ever imagined she would be launched."
1803 - 1804: The Peace of Amiens and an anxious journey through France and Spain after hostilities resumed delay Jack's assignment in Post Captain to a new command until he is given the very unconventional ship-sloop HMS Polychrest, an unusual vessel with sharp ends at both bow and stern, no tumblehome (inward curvature at the top of the hull), drop keels (similar to daggerboards on some modern sail boats), and the remnants of the launching system for an unsuccessful secret weapon (a giant rocket). After several months of service in the English Channel, the Polychrest is severely damaged in a raid on a French port and sinks soon thereafter.
The physical form of the Polychrest (except for the secret weapon) was taken from the Dart class of sloops. The sliding keels, originally designed by Captain Schank, were employed upon a number of small Royal Navy vessels around this period, although problems with leaking centerboard cases perhaps discouraged wider experimentation. Unlike the Polychrest with its extraordinary leeway and a propensity for missing stays, the real HMS Dart and her sister ship Arrow performed satisfactorily during their Royal Navy service. The Dart was broken up in 1809. The poor sailing qualities of Polychrest and perhaps the notion of a new secret weapon were likely taken from HMS Project, a much smaller vessel than the Dart (and Polychrest) with a very shallow draft to carry a new design of howitzer into coastal waters. The Project was broken up in 1810 after only five years of service.
"No wonder they called her a crack frigate: her sailing qualities were quite out of the ordinary, and the smooth quiet discipline of her people was beyond anything he had seen."
1804 - 1805: Jack's success in raiding the French port, despite the loss of the Polychrest, brings him promotion in Post Captain to the rank of, naturally, post captain and the temporary command of the 38-gun frigate HMS Lively. With the Lively Jack takes part in the interception of a Spanish treasure squadron in the Atlantic. After participating in blockade operations in the western Mediterranean in H.M.S. Surprise, Jack Aubrey relinquishes command of the frigate to her regular captain and returns home to England.
The Lively was a genuine Royal Navy ship. However, Patrick O'Brian did alter the ship's history for purposes of his fiction. In Post Captain the frigate is described as having served for a considerable period in the East Indies when in fact the Lively was launched and commissioned in 1804, the same year when Jack Aubrey takes command. The Lively was lost in a wreck near Valletta while escorting a convoy to Malta in 1810.
"... he knew her through and through, as beautiful a piece of ship-building as any that had been launched from the French yards, a true thoroughbred, very fast in the right hands, weatherly, dry, a splendid sailor on a bowline, and a ship that almost steered herself once you understood her ways."
1805 - 1806: Through the intervention of Stephen Maturin at the Admiralty in H.M.S. Surprise, Jack Aubrey is given the small frigate HMS Surprise of 28 guns, aboard which he had served years before as a midshipman. His assignment is to carry a diplomat to the East Indies, where he uses his ship to support the China Fleet of East India Company merchantmen to successfully fight off Admiral Linois's squadron. Afterwards, Jack and the Surprise return across the Indian Ocean to the Atlantic and head northwards towards home.
HMS Surprise is another genuine Royal Navy ship, although with a rather different history than that portrayed in O'Brian's novels. The historical Surprise was originally the French l'Unite, captured in 1796. Although this accords well with Jack's comment that she had been taken from the French "early in the last war" (evidently meaning the French Revolutionary War, beginning in 1793), Jack's other descriptions of her past do not so well match history. His mention of having served aboard her as a midshipman would require her service in the Royal Navy during the 1780's, and his frequent references to her great age are not appropriate for a ship launched in 1794. (In a later novel, however, by way of contrast Jack does refer to her capture by the Royal Navy in 1796.) In one important aspect the fictional description of the Surprise agrees with history: while Captain Edward Hamilton had been in command, he ordered the installation of a mainmast of a size usually specified for a 36-gun Fifth Rate frigate, giving her a unique appearance. The real Surprise was sold out of the service in 1802, three years before Jack Aubrey fictionally takes command. The action of Linois against the China Fleet was genuine, although the real Surprise did not take part, and it actually occurred in 1804 while the fictional Jack Aubrey was still in command of the Polychrest.
A note about armament: Although records are complex, Rif Winfield's research indicates that when the Surprise was initially taken into the Royal Navy in 1796 in the Mediterranean, she was classified as a Sixth Rate of twenty-eight guns. The following year she was deployed to Jamaica and, while there, was converted into a Fifth Rate (although not re-registered as such) with twenty-four 32-pound carronades and eight 18-pound carronades, and a crew of 240. In 1798, probably during her refit at Plymouth, the Surprise was once again converted to a 28-gun Sixth Rate, armed and crewed as stated in the description of her draught. [Information from a private communication to Bruce Trinque from Rif Winfield]
A note on the deck diagrams: The deckplans and the longitudinal section of the Surprise, showing her as she was while in the Mediterranean during The Ionian Mission in the Long Year of 1813, are courtesy of Bruce Trinque and can be explored in further depth here. These plans are based upon the actual Admiralty drawings of her hull, with details of her inner layout drawn from other Royal Navy frigates of the era and from descriptions within the pages of Patrick O'Brian's novels.
"... the Boadicea proved she was a dry, wholesome ship."
1809 - 1810: At the opening of The Mauritius Campaign, Jack has been ashore for a lengthy period of time, very probably since he left the Surprise. Again through the action of Stephen Maturin at the Admiralty, Jack Aubrey is given command of the 38-gun frigate HMS Boadicea, with the prospects of being commodore of a squadron of ships to be directed against Mauritius and the nearby islands in the Indian Ocean. After the successful conclusion of the campaign, Jack is ordered home in his ship to carry the happy news.
Boadicea is another real Royal Navy ship, and there is nothing in O'Brian's description of her which conflicts with her genuine history. In fact, the Boadicea was Commodore Josias Rowley's ship in the Royal Navy's Mauritius campaign, in which Rowley actually performed the activities assigned in the novel to Jack Aubrey. She was eventually broken up in 1858.