- Aluminum Christmas Trees: Aubrey's crews can sometimes seem like Politically Correct History, but it was commonplace at the time for the Royal Navy to recruit any able seamen they could find, be they white, black, Chinese or even French. Early in his command, to get his point across to a couple of pressed American sailors, Jack promotes a black sailor to bosun's mate.
- Big-Lipped Alligator Moment:
- At one point in The Far Side of the World, Jack and Stephen are separated from their ship in a lifeboat, and are picked up by a catamaran full of lesbian Polynesians who have apparently recently castrated their husbands and nailed their testicles to the front of their boat. They are let loose without much incident, with no plot consequences, and it's not even played for fanservice. Its main purpose seems to be a giant setup for the image of a female Maturin striding across England with a flaming sword 'castrating left and right'.
- Jack and Stephen's escape from France in Post Captain where Stephen makes a bear disguise for Jack, and Jack has to walk hundreds of miles on all fours out of France to cross into Stephen's ancestral home in Catalonia. The emergence of the furry fandom since the book was published has resulted in a Hilarious in Hindsight view of the event that Stephen rescued Jack by making him wear a fursuit.
- Contested Sequel: Fans who come to the series for the bloody and tense Wooden Ships and Iron Men action in "Master and Commander" can struggle with the following book "Post Captain" which spends a large part of its pages as a tribute to Jane Austen with a land-based romance plot (and when it does return to wartime stories it can get rather offbeat with a bizarre prototype ship that sails backwards, an angry swarm of bees and a daring escape while wearing a fursuit). Many fans suggest skipping straight ahead to the "HMS Surprise" which more clearly captures the tone of the rest of the series, yet ardent "Post Captain" defenders point out the work the book puts into fleshing out the main characters as critical to the rest of the series.
- Diagnosed by the Audience: Maturin's general lack of finer social queues, his obsessive attitude towards naturalism, and his strict (if somewhat warped and contradictory) sense of morality has had some fans speculate he is somewhere on the autism spectrum. His daughter Brigid showing severe autistic traits as a child also suggests some genetic traits shared in the family. Nathaniel Martin also shows similar traits, and he bonds deeply with Stephen over their shared interest in naturalism and it offers Stephen a reprieve on several voyages from the naval social world.
- Genius Bonus: Jack shares his initials with author Jane Austen who was a major inspiration for O'Brian.
- Hilarious in Hindsight:
- At one point Jack asks Stephen to check up on his current crew's religious affiliation after one sect's beliefs threaten to cause trouble. Stephen's report includes the fact that Jack's cook "worships the Devil" (he's a Yazidi, a Caucasian sect who believe Satan repented). In the late 2000s a controversy emerged over the Royal Navy employing an actual Satanist.
- On one occasion, (described in one of the earlier books written in the 1970s), Stephen leaves some important secret papers behind in a hired carriage, which causes him much distress and embarrassment (though the papers are later retrieved). In 1990, during the run-up to Desert Storm, a British officer left a portable computer containing important classified documents on Coalition plans in a car he had been test-driving; the computer was soon recovered in that case as well.
- In 1996's "The Yellow Admiral" Diana after driving a carriage, stops at an inn announcing her intention to have a "second breakfast." One of her carriage passengers at the moment is Barrett Bonden who in Master and Commander is portrayed by Billy Boyd, whose portrayal of Pippin Took in The Lord of the Rings: The Fellowship of the Ring would also get memetically associated with second breakfast.
- Nightmare Fuel:
- The fate of the Waakzaamheid in Desolation Island. After a days-long Stern Chase through the South Atlantic in a howling storm, one of the rear guns on the Leopard finally gets off a lucky shot that takes out her pursuer's foremast. The mast topples overboard and immediately drags the Waakzaamheid under, with no survivors. Watching it happen, Aubrey has a "My God, What Have I Done?" moment.
- The shipboard outbreak of "gaol-fever" (i.e. typhus
), in Desolation Island, makes for tense reading.
- Squick:
- In Master and Commander, there's an incident in which Maturin is having dinner with a fellow doctor who has just been dissecting an ape. Maturin looks for a sharp knife to cut his beef, and finally finds it under the body of a young woman that the other medico has been autopsying, having first checked under a dolphin's flipper. When his dinner companion wonders if the knife should be washed, Stephen casually replies that all it needs is a wipe.
- Stephen has very casual attitudes toward the corpses or parts of corpses he acquires for study. This produces an amusing moment in one of the later books where Stephen sets aside the body of one of his patients for later dissection just before a sea battle, and it gets buried at sea along with the regular KIA's, much to his dismay. His ghoulish tendencies are a large part of the reason he and his wife Diana keep separate houses: she has a much less understanding attitude towards a pancreas in the sock drawer.
- When searching in Stephen's pack for a pistol, Jack pulls out a jar with a teratoma inside. He is understandably disturbed.
- The way Stephen disposes of two enemy intelligence agents who have caused him and Jack considerable troubles: he shoots them and then dissects the bodies with his natural philosopher friend in order to dispose of the evidence.
- In The Mauritius Command, Stephen asks Killick to stick out his tongue during a medical checkup, and it's described as "a flannelly object of inordinate length".
- Stephen's 'Hand of Glory' (a preserved hand with a strange case of calcified tendons) is eaten by the marine captain's dog. Stephen values the hand so much that he purges the dog and retrieves the bones and tendons from the...resulting mess.
- During Clarissa Oakes/The Truelove the crew visits a Polynesian island where ritual cannibalism is practiced. After helping the local queen defend her throne from an usurping tribe the crew gathers for dinner; only for one of them to be mistakenly handed a bowl containing meat from the slaughtered leader of the rebels. The queen laughs it off as a mistake and the British crew is served pork instead.
- Tear Jerker:
- In The Hundred Days:
- All the more devastating because it's reported in such a bald and matter-of-fact manner: Barret Bonden, Jack's coxswain and also a close friend of Stephen's, who has been with the duo ever since the first book, is killed in action.
- Diana, Stephen's wife, his partner in a complex and tumultuous romance spanning most of the series, is killed offstage in a carriage accident. We are mostly left to imagine the devastation Stephen must feel.
- As we've seen throughout the series, very young boys (as young as eight, in some cases, and probably even younger in at least one case) serve as midshipmen aboard Royal Navy vessels, and are subject to the same dangers and hazards as their adult shipmates. Their maimings and deaths cause considerable anguish to Jack. He calls them mice, because they're so small and cute and likely to piss and shit everywhere.
- In The Hundred Days:
- The Woobie:
- In a series of novels spanning over a decade with hundreds of characters, almost all the principal characters fall under this category at one point or another.
- Stephen. Where to start? He pursues a woman for years, at one point very nearly fighting a duel with Jack — his closest friend — over her. He actually fights a duel over her in India, killing a man who might in other circumstances have become a close friend. He finally wins the lady, only to have her leave him — temporarily — because she thinks, mistakenly, that he has humiliated her with another woman in Malta. His daughter, for now at any rate, seems autistic. And finally, the woman dies in a carriage accident offstage. Not to mention that he gains and loses a fortune several times, and he almost dies from the sting of a (male) platypus, an animal he has longed to see for as long as he has been a naturalist.
- Many more minor characters over the course of the series - there's Cheslin the sin-eater in the first book, and that failed cutpurse in the second. An in-universe example was Mr. Hollom, who was never given a lieutenant's commission and so is still a midshipman in his late thirties, increasingly as he ages thought worthless and "a Jonah", no captain will accept him on board so he's left on land (oh, and midshipmen get paid nothing whatsoever if they're not serving on board a ship). Jack knows he won't fit in in the midshipmen's berth and knows the crew will consider him unlucky, but can't keep himself from letting him on board (though he mentally grumbles, "Oh this is G-ddam blackmail").
- In the movie, Hollom accepts his role as Jonah, grabs a cannonball, and steps overboard, drowning himself. The becalmed ship is almost immediately given a gentle, rain-soaked wind, even as Jack admonishes the crew for their treatment of the older midshipman.
- Lord Clonfert in The Mauritius Command qualifies, being a genuinely capable and courageous officer who is crippled by an undetermined mental affliction (thought to be bipolar disorder), and who agonizes over his self-perceived inadequacy when placed next to men like Jack and Cochrane. An English-born noble with an Irish title, Clonfert was struck off the Navy list and only recently reinstated, forced to serve under a man who used to be his subordinate. His anxiety to be popular with his men and desire to be as successful and dashing as his idol Sir Sidney Smith prompts him to make foolish choices. He loses his ship and is hideously disfigured in a bungled engagement with the French. As he recovers in the hospital, he learns of Jack's successful conclusion to the campaign. Unable to bear the shame of his failure and yet another instance proving Jack's unconscious superiority, Clonfert purposefully reopens a dangerous wound and bleeds to death. While Clonfert's surgeon and friend tearfully blames Jack for Clonfert's death, Stephen reflects "You cannot blame the bull because the frog burst: the bull has no comprehension of the affair."
- Stephen is approached by a young post captain who is suffering from PTSD, having fired upon a galley rowed by chained slaves, sinking the galley and sending the men to their deaths. He is haunted by the memory of their faces, and questions his suitability for command. Soon after, the same captain 'accidentally' kills himself while cleaning his pistols.
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