Synopsis
During the Napoleonic Wars, Captain Jack Aubrey of HMS Surprise is ordered to intercept the heavy frigate Acheron, a French privateer. Acheron ambushes Surprise off the coast of Brazil, causing heavy damage while remaining undamaged by the British guns. The ship's boats tow Surprise into a fog bank to evade pursuit. Aubrey's officers tell him that Surprise is no match for Acheron, and that they should abandon the chase. Aubrey responds that Acheron must not be allowed to plunder the British whaling fleet and orders Surprise refitted at sea, rather than a lengthy return to port for repairs. Midshipman Blakeney has his arm amputated due to injuries sustained in battle. Shortly afterward, Acheron again ambushes Surprise, but Aubrey slips away in the night by using a decoy raft and ship's lamps.
Following the privateer south, Surprise rounds Cape Horn and heads to the Galápagos Islands, where Aubrey is convinced that Acheron will prey on Britain's whaling fleet. The ship's surgeon, Stephen Maturin, is interested in the islands' unique flora and fauna, and Aubrey promises his friend several days' exploration time. However, when Surprise reaches the Galápagos, they recover the survivors of a whaling ship destroyed by Acheron. Aubrey hastily pursues the privateer, dashing Maturin's expectation of more time to explore.
Surprise is becalmed for several days. The crew becomes restless and disorderly, and superstition begins to take hold among them. Midshipman Hollom, already unpopular with the crew, is named a "Jonah" by the sailors (someone who brings bad luck to a ship). As the tension rises, crew member Nagle deliberately bumps shoulders with Hollom as he passes him on the deck and is flogged for insubordination. That night, Hollom commits suicide by jumping overboard with a cannonball; Aubrey holds a service for Hollom the next morning. The wind picks up again, and Surprise resumes the chase.
The next day, Royal Marine officer Captain Howard attempts to shoot an albatross but accidentally hits Maturin instead. The surgeon's mate informs Aubrey that unless the bullet and a piece of cloth it took with it are removed soon, they will fester. He also recommends the delicate operation be performed on land. Despite closing on Acheron, Aubrey takes the doctor back to the Galápagos. Maturin performs surgery on himself using a mirror. Finally giving up the pursuit of the privateer, Aubrey grants Maturin the chance to explore the Galápagos Islands and gather specimens before they head for home. While looking for a species of flightless cormorant, the doctor discovers Acheron on the other side of the island. Maturin abandons most of his specimens and hurries to warn Aubrey. Surprise readies for battle once more. Due to Acheron's stronger hull, Surprise must be at close quarters to damage her. After observing the camouflage ability of one of Maturin's specimens, Aubrey disguises Surprise as a whaling ship; he hopes the French will be lured in to capture the valuable ship rather than destroy it. Acheron falls for the disguise, and Surprise launches her attack. With the back wheels of the cannons taken off, the cannons are angled upward and fire upon Acheron's mainmast while Captain Howard's Marine sharpshooters pick off the crew of Acheron from above. Acheron is disabled when the mainmast snaps and falls into the sea. Aubrey leads boarding parties, engaging in fierce hand-to-hand combat. Upon capturing the ship, Aubrey is informed by the ship's doctor that the French captain is dead and is given the Captain's sword.
Acheron and Surprise are repaired and Surprise remains in the Galápagos. Pullings is promoted to captain and ordered to sail the captured Acheron to Valparaíso. As Acheron sails away, Maturin mentions that their doctor had died months ago. Realising the French captain deceived him by pretending to be the ship's doctor, Aubrey gives the order to change course to intercept Acheron and escort her to Valparaíso, and for the crew to assume battle stations. Maturin is again denied the chance to explore the Galápagos, but Aubrey wryly notes that since the bird he seeks is flightless, "it's not going anywhere." The two then play Musica notturna delle strade di Madrid by Luigi Boccherini as Surprise turns in pursuit of Acheron once more.