- As HMS Surprise is rounding Cape Horn, one of the seaman, Wharley, is washed overboard whilst trying to secure a flapping sail to one of the masts. As he swims towards the wreckage of the mast, still attached to the ship by its rigging, it is revealed that the wreckage is pulling the ship under, threatening to sink her and kill all her crew. Captain Aubrey must make the decision to cut the ropes and sacrifice Wharley to save the ship, doing so along with the Ship's Master, and also Wharley's best friend Nagle. As Jack cuts the last rope and the wreckage floats free, we see Wharley, still swimming, disappear behind a large wave. This is accompanies by Vaughan Williams' "Fantasia on a Theme," and made even more powerful as the scene cuts to the rest of the crew below decks celebrating their survival, oblivious to Wharley's death. We then see Nagle sorting Wharley's possessions and shutting them in his sea chest, including a sketch he had done for his sweetheart with the words "Home Again".
- Even worse as you watch just before the last rope is cut, Warley is only a few feet from the mast. When it's cut, the mast is swept away by the storm. Had he been just a little faster, he likely would have survived and been able to reach shore.
- Aubrey and Maturin's falling out when he is forced to break his promise of indulging the scientific curiosity of his friend for the sake of the mission. You can see Crowe's character grappling marvelously with the inner conflict. And Bettany is comparable to a kicked puppy in his tangible disappointment and angered forlornness.
Dr. Maturin: Jack, have you forgotten your promise?
Capt. Aubrey: Subject to the requirements of the service. I cannot in all conscience delay for the sake of an iguana or a giant peccary. Fascinating no doubt, but of no immediate application.
Maturin: There is, I think, an opportunity here, to serve both our purposes. As I understand it, this is a long thin island. You need to sail around it in order to continue your voyage. I could walk across it; I'd be on the other side long before you—
Aubrey: Stephen. I have known you to spend hours staring into a deserted bird's nest.
Maturin: [agitated] I could walk briskly, pausing only to take the most important measurements, certainly making valuable discoveries that could help advance our knowledge of natural history.
Aubrey: If wind and tide had been against us, I should have said yes. They're not; I'm obliged to say no.
Maturin: ... Oh, I see. I see, so after all this time in your service I must simply content myself to form a part of this belligerent expedition, hurry past inestimable wonders, bent solely on destruction, I shall say nothing of the corruption of power, or its corrup—
Aubrey: [warning, dismissive] You forget yourself, Doctor.
Maturin: No, Jack, no. You've forgotten yourself. You see for my part, I look upon a promise as binding.
Aubrey: The promise was conditional.
Maturin: It never occurred to me until you had to say—
Aubrey: I command a king's ship, not a private yacht!
Maturin: This would never have happened when we were of the same opinion!
Aubrey: WE DO NOT HAVE TIME FOR YOUR DAMNED HOBBIES, SIR!
Maturin: ... [stares him down, drenched in sweat and white-faced, turns his back on his friend and promptly quits his cabin]
Aubrey: [instantly regretful and furious with himself]
- The aftermath of the final battle is also a tearjerker (with Vaughan Williams again contributing). We see the dead lined up on the deck being sewn into their hammocks... including Nagle, and also teenage Midshipman Calamy, just promoted to Acting Lieutenant. Traditionally, the dead are prepared for burial by their messmates, and Calamy's friend and fellow Midshipman, 12-year-old Blakeney, looks on, before asking if he can do the final stitches. Having lost his arm earlier, he is unable to, and needs help from "Awkward Davies," a large, dangerous brute, but incredibly loyal to his Captain, who does so without words. We then get the funeral service, where Aubrey reads out the names of the dead, stumbling slightly at the ship's Sailing Master, Allen, then choking as he reads out "Peter Miles Calamy, Lieutenant."
- Hollom's entire character arc, from being still a midshipman at nearly thirty, to coming to believe he is a Jonah thanks to his treatment at the hands of the men, to killing himself.
- The suicide scene. And his choice to let it be witnessed by the one person, the one twelve-year-old boy who's been nice to him, and saying goodbye...
- Any time Ralph Vaughn Williams' beautifully mournful "Fantasia on a Theme" by Thomas Tallis kicks up, expect waterworks.