In 1805, in the midst of the Napoleonic Wars, the Royal Navy frigate, Captain Aubrey of HMS Surprise is ordered to pursue and destroy the French privateer Acheron, bound for the Pacific.In the opening scene, a midshipman briefly sees a dark shape in a fog bank and calls for the captain. As Aubrey scans the fog bank with his spyglass, the Surprise is suddenly raked by cannon fire. The Acheron appears and the Surprise is hit repeatedly, causing severe damage and many casualties. In the calm, Aubrey orders the Surprise to be towed into the fog bank where she evades the Acheron.After inspecting the damage, Aubrey decides to refit the ship as best they can at sea, and pursue the Acheron. The crew works to repair the ship while Dr. Maturin works hard to save the lives of the casualties including a young midshipman, whose arm he has to amputate. The Surprise resumes its pursuit but the Acheron again surprises them and they begin a day long pursuit. As night falls, Acheron begins firing. By placing lights on a decoy raft, resembling the lights of the Surprise, they again evade the Acheron. As they approach Cape Horn, the Surprise is closely following the Acheron, but they lose sight of the Acheron as both ships bring in sail in rising winds. A sailor is lost in the raging seas when the mizzen topmast breaks in the storm. Aubrey tells his officers that he is heading for the Galapagos Islands, where he is certain the Acheron will be as that it is where Britain’s whaling fleet may be found. Maturin later tells Aubrey that the Galapagos are legendary to Naturalists such as himself. Aubrey promises the doctor that he will be granted several days of exploring on the islands. When the Surprise reaches the islands, they find and recover the surviving crew of the Albatross, a whaling ship, burned by a “big, black three-master”. Jack orders all hands to make sail to pursue the Acheron. This annoys the Doctor, who protests that Aubrey is breaking his word to let him explore. Some days into their voyage from the Galapagos, Surprise is becalmed. A seaman Nagle is disrespectful and insubordinate towards Midshipman Hollom. Jack witnesses this and orders that Nagle be flogged for disobedience, and later chastises Hollom for failing to prevent this. Later Hollom, believing himself to be a Jonah as he has been involved in many unfortunate incidents on the voyage, commits suicide by jumping into the ocean. Dr. Maturin is accidentally shot by Marine Captain Howard and loses consciousness. The surgeon's mate informs Jack that unless the bullet can be removed Maturin will die, but to safely perform the surgery they need to be on land. A sail is spotted on the horizon ahead, believed to be the Acheron. Aubrey is now faced with a difficult choice: follow the ship, or save his friend. When Stephen regains consciousness, he realises that they have returned to the Galapagos and Aubrey has abandoned his pursuit in order to save him. The Doctor performs the surgery on himself with the aid of a mirror. He succeeds in removing the musket ball and recovers quickly. He now has the opportunity to explore the Galapagos. He makes many scientific discoveries, including a type of flightless cormorant. From the top of a hill, he notices a large three-masted ship sailing into one of the island bays flying the French flag. The Acheron has returned. During their return to camp, Maturin's bullet wound slows him down, forcing Padeen, his assistant, to release the specimens and carry the Doctor back to camp. Surprise is disguised as a whaling ship. The Acheron takes the bait chasing the Surprise. As the French ship comes alongside, the Surprise opens fire and the Acheron’s mainmast falls, the Surprise crosses the Acheron's stern, raking her and inflicting many casualties and upsetting her cannon. Leaving the "Surprise" under the command of Blakeney; Jack and Lieutenant Pullings lead the boarding parties but are ambushed themselves. Master Allen, Nagle and many of the Surprise’s crew are killed. After seizing control of the ship, Aubrey searches the Acheron for her captain and is directed to the sickbay, a man introducing himself as Docteur de Vigny tells him that the French captain has been killed. The Acheron and Surprise are repaired. Jack gives command of the Acheron to Pullings, naming him ‘Captain’ Pullings, ordering him to take the French ship to Valparaiso, while the Surprise returns to the Galapagos. As the Acheron sails away, Aubrey tells Maturin of his talk with de Vigny. Maturin tells him that de Vigny had died months ago. Aubrey gives orders to pursue the Acheron, Maturin is again denied the chance to explore the Galapagos. Jack notes that since the bird he seeks is flightless, it "isn't going anywhere." The film is constructed from episodes from several novels in Patrick O'Brian's Aubrey-Maturin series. The main plot, in which Aubrey in HMS Surprise chases an enemy frigate round Cape Horn into the Pacific, is based loosely on The Far Side of the World, but the American frigate USS Norfolk in the book becomes the American-built French privateer Acheron in the film (the Acheron is based on 44-gun American frigates like the USS Constitution). The stern chase around Cape Horn is taken from the novel Desolation Island, although the Acheron replaced the Dutch ship of the line Waakzaamheid, the Surprise replaced the Leopard and in the book it is Aubrey who is being pursued around the Cape of Good Hope. The episode in which Aubrey deceives the enemy by means of a raft bearing lanterns is taken from Master and Commander, and the episode in which Maturin operates on himself to remove a bullet is taken from HMS Surprise. The film is largely faithful in plot to the novels, although there are a few major departures from the series. In the movie, Stephen Maturin inadvertently gives Jack Aubrey the inspiration to disguise Surprise as a whaling ship to fool an enemy, implying that this is a new idea for Aubrey. However, in the first Aubrey/Maturin book Master and Commander, Aubrey regularly uses the tactic of disguising his ship during his very first command, and it is described as a common tactic used by warships to approach unsuspecting targets and avoid attention from larger enemy ships. The exploit of setting up a decoy of a large ship at night by attaching lights to a small boat was executed by the French privateer Robert Surcouf to successfully escape the British frigate HMS Sybille. It was also used by Lord Cochrane and described in his Autobiography of a Seaman, which was used by Patrick O'Brian as source material for his novel Master and Commander. In that novel, Jack Aubrey's first command, HMS Sophie escapes by using this tactic, while in the film it is Surprise which escapes Acheron using this trick. The movie gives the impression that Jack Aubrey promotes his first lieutenant, Pullings, who receives his new captaincy with joy. In fact only the Admiralty could make such promotions, and the difficulty obtaining them is a recurring theme in the books. This was especially true for men such as Pullings, who as a member of a lower class without money or social connections might spend years hoping in vain for advancement. It was, however, possible for Captains (such as Aubrey) to make a lieutenant an Acting Captain for the duration of the commission — which was usually until the ship (in this case, the captured Acheron) arrived with all-important dispatches back in London (something which usually merited a promotion), and which is where Pullings is bound for — eventually — at the end of the film. In the novel, Pullings has already been promoted to Commander, but has not yet been given a command of his own. He accompanied Captain Aubrey on this mission in order to avoid being left on shore with nothing to do, as well as improve his prospects for being given command of a ship by demonstrating his zeal for king and country. Nowhere in the Aubrey/Maturin series of novels is Dr. Maturin shot by a Royal Marine. However, in the novel "H.M.S. Surprise" Maturin fights a duel with a Mr. Canning, a rival for Maturin's affections for Diana Villiers. Although Maturin is deadly with both sword and pistol, and kills Canning, he is wounded in the exchange and operates on himself to remove the deflected bullet from his chest. Probably the largest difference between the film and the books is the profession of Stephen Maturin. In the books he is a spy for England (as well as being a physician and naturalist), but although several references to both his beliefs and to espionage in general are made, he is never shown to be a spy. The film also plays out the role of Hollom as a Jonah to a much greater extent. Hollom is shown ending his life by jumping over the side with a cannonball in his hands, whereas in the book he is presumed murdered by Horner, the ship's Gunner, when Hollom instigates and consummates an affair with Horner's wife. This romantic triangle was removed from the plot in the film. The first two and final three chapters of The Far Side of the World do not appear in the film. Also, the prominent scene of Warley being sacrificed on the order of Capt. Aubrey does not appear in any of the books, and a substantial majority of the movie dialog is created by scriptwriters Weir and Collee.

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