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  • Aluminium 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.
  • Bittersweet Ending: More meta than actual. Blue at the Mizzen was Patrick O'Brian's last completed book in the Aubrey/Maturin series before he died in 2000. While the book's ending couldn't be any happier Jack finally earns promotion to his long-coveted admiral's rank, entitling him to fly his blue admiral's ensign at the mizzenmast; this causes a very emotional moment between Jack and Stephen, who brings him the joyous news personally, it's also a slightly melancholy moment for fans who know that this is basically where the epic ends.
  • 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'.
  • 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 another 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.
  • Ho Yay: Oh so very much.
  • 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), earlier in the same book, makes for tense reading as well.
  • Squick: Not all that many examples in the series, considering the often-gruesome nature of the wounds Maturin has to treat; however, 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.
    • In fact, most of the examples of Squick in the series have to do with Stephen's 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 he 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.
  • Tear Jerker:
    • 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 in The Hundred Days.
      • Also in the same book: 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 (also providing examples of his being A Father to His Men).
      • Of course, in actual combat, as opposed to overarching military strategy, neither man pulls any punches until the opposition is dead or surrenders. Jack will burn a ship to the waterline and slaughter an entire crew if they can't be compelled to surrender, be happy about the victory, then toast to the fallen after the battle, while Stephen is perfectly capable of standing face to face in personal combat, or slitting his enemies' throats in their sleep.
  • Values Dissonance: Or, more accurately, Deliberate Values Dissonance.
    • Although it's considered to be a bad thing, Aubrey is never especially perturbed that his sailors are often arrested for rape once they get back on shore.
    • Aubrey, being British, is not too fond of the American Revolution, either.
      • Aubrey is a Tory (in today's terms, a Conservative). Whigs (today's Liberalsnote ) were generally sympathetic toward the American cause. Most Americans today don't know that the American Revolutionary War was pretty much as politically divisive for 1770s Britain as the Vietnam War was for 1960s America.
    • On one occasion after the War of 1812 ends, when the Surprise has just concluded a friendly exchange with an American frigate, Aubrey scoffs at the Americans as "little better than democrats" (in that era, "democracy" was considered to be a grossly inferior form of government by many educated people trained in Aristotelian views) before going on to make complimentary remarks about the particular American frigatemen.
    • Also note that Aubrey, despite his low opinion of the American system of government, thinks the War of 1812 to be a terrible tragedy and gross mistake even though he does his duty. (It's noted that his opinion is shared by many other Royal Navy officers.)
    • In Desolation Island, set just before the War of 1812, Jack is commanding the HMS Leopard, the same ship that notoriously fired on the USS Chesapeake in 1807 to force it to hand over British nationals who were serving in its crew (and almost started a war at that point); Jack freely acknowledges, if mainly in his thoughts, that the British were in the wrong in that incident and that he would have been infuriated at the insult to his country and service had he been American. His command of the Leopard sets up a Chekhov's Gun incident in the next book, The Fortune of War, where he falls under suspicion by the Americans for that reason, being at one point falsely accused of having fired on an American vessel in peacetime.
    • Aubrey also turns a blind eye to a seaman's particular sexual practices in the first book, despite the Article of War which mandates the death penalty (for * cough* sodomy * cough* )- but he does ensure that the goat the man practiced upon gets a clean and painless end.
      • Throughout the series, Jack generally tends to take a live-and-let-live approach toward homosexuals in the Royal Navy; for instance, his main concern about a gay captain in his squadron in The Commodore is not his sexual orientation, but the bad effect on discipline and order that results from the captain's showing undue favoritism toward his partners.
    • Throughout most of the series Aubrey has an indifferent view to slavery, one similar to his hero Nelson. That changes drastically in The Commodore. He captures a slave ship and comes face-to-face with the horrors of the Middle Passage. He has some of the slavers arrested, forcibly issued with mops, and thunders at them to clean up the filth on the lower decks.
    • Stephen is a fervent abolitionist. He never quarrels with Jack about the subject, but in a Noodle Incident he verbally savages a slaveholder in the West Indies to the point that Jack was surprised that Stephen wasn't called out for a duel.
      • Stephen, in The Wine-Dark Sea, is reported to be a subscriber to a project to resettle freed slaves in Sierra Leone. While many modern observers today view such schemes with suspicion as being at least potentially racist in motivation, those projects were extremely popular among anti-slavery activists in the first half of the 19th century (Abraham Lincoln, for example, supported the American Colonization Society's efforts to resettle emancipated slaves in Liberia).
    • In HMS Surprise neither Stephen nor Diana seems particularly bothered that the Indian girl Stephen befriends in Bombay is for sale. Diana's only comment is that Stephen should really only pay a quarter of the asking price.
    • This being the early 19th century, before Catholic emancipation, Stephen regularly encounters casual anti-Catholic prejudice among the Anglican Englishmen he encounters, including even Jack (though this is unintentional on Jack's part, he sometimes blunders verbally, much to his dismay and embarrassment). Stephen has developed a thick skin over the years for this kind of talk, so he almost always waves it off, sometimes making a quip in reply. (This is, of course, providing that it's essentially unintentional and that his interlocutor apologizes quickly; Stephen will take offense if it's deliberate.) Ditto cracks about the Irish, as one unfortunate officer at a dinner party found out...
      • Jack gets a little better about this after he meets his illegitimate son, Sam Panda, who is Catholic and becomes a priest.
    • Jack, along with most of his fellow Englishmen, are prone to making unthinkingly bigoted remarks about just about anyone not English. It's important to note, though, that Jack acts far less bigoted than he talks.
      • The Surprise is explicitly described on numerous occasions as carrying a multiracial, polyglot crew, and it's Jack's invariable practice to treat everyone of a given rank equally.
      • Jack never treats his illegitimate son, Sam Panda, borne by an African woman with whom he had an affair early on in his career, with anything other than deep affection and respect. When he and Sam first meet, he frets over the possibility that Sophie might get angry, but in fact she proves to be broader-minded than that and accepts him readily, particularly as the liaison that produced him took place many years before Jack and Sophie ever met.
    • The sailors on the various ships that Jack and Stephen sail on are prone to slaughtering the birds and animals of the remote places they visit by their thousands and tens of thousands, for food or just for sheer bloody-minded fun. Stephen himself is a keen hunter, for food gathering or for obtaining scientific specimens, but he's closer to modern sensibilities in that he sharply objects to the wanton slaughter of animals, especially if it doesn't have any rational purpose such as obtaining food.
    • Stephen is a very open-minded and tolerant individual. However, being half-Catalan, he cannot abide a Moor (though he never actually has to deal with one).
    • One particular personality conflict between Jack and Stephen sets them apart, in terms of their approach to the strategy of combat: Jack is all about fighting as per the laws and customs of war at the time, with the biggest ruse he's willing to do being sailing under false colours note , and will not violate them. Stephen, on the other hand, is very much a practical strategist, willing to sabotage his opponent at every stage, and calls out the ridiculousness of being willing to sail under false colors but not to read an opponent's letters. Though they eventually come to see eye-to-eye through character development. During the Hundred Days they have a long conversation on the matter after Stephen arranges for dockworkers in the Balkans to burn French ships at drydock, and Jack concedes that it is better to destroy the ships this way, as there is far less loss of life.
  • 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").
    • 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.
    • Dil. Just, Dil.

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