The story starts out on April 18, 1800, in
Port Mahon, Minorca, a base of the Royal Navy at that time. A shipless lieutenant wasting away in port, Jack Aubrey, meets Stephen Maturin, a poor half-Irish and half-Catalan physician and
natural philosopher, at an evening concert at the Governor’s Mansion. The two of them do not quite get along during this first encounter. A duel almost occurs when Jack Aubrey gets elbowed by Maturin to stop humming while the string quartet is playing.
Later that evening, on his way back to his living quarters, Jack Aubrey finds out that he was promoted to the rank of Commander and has been given command of the
sloop Sophie. His joy overcomes his animosity towards Stephen Maturin and they quickly become good friends. The ship's surgeon having left with the previous captain, Maturin is asked by Aubrey to sign on in that post. Although Maturin is a physician, not just a mere surgeon, he agrees, since he is currently unemployed.
Also introduced into the story are Master's Mates Thomas Pullings, William Mowett, midshipman William Babbington, and James Dillon, the
Sophie's first lieutenant. Dillon has a secret background as a member of the United Irishmen which crosses with Stephen's own.
Aubrey improves
Sophie's sailing qualities by adding a larger yard which allows him to spread a larger mainsail. She then is sent to accompany a small convoy of merchant ships. During their journey east, the new captain, Aubrey, takes the opportunity to get to know his sailors and work them into a fighting unit. As he does this, he and the crew explain many naval matters to Maturin (and to the reader) since the doctor has never served aboard a man-of-war.
After the convoy duties,
Lord Keith allows Aubrey to cruise independently, looking for French merchants. After a number of prizes are taken, they meet and defeat the
Cacafuego, a Spanish frigate, losing a number of crew, including Dillon, in the bloody action and gaining the respect of other naval officers. However, Captain Harte, the commandant at Mahon, has a grudge against Aubrey, who has been having an affair with his wife. His malevolence ensures the victory brings Aubrey and his crew no official recognition, promotion, or significant prize money.
On her following escort duty, Sophie is captured by a squadron of four large French warships after a pursuit and a brave but hopeless resistance.
The Battle of Algeciras begins, and after a short period as prisoners of war, they are exchanged, missing the fighting. Back at Gibraltar, Aubrey must undergo a court-martial over the loss of his ship, but he is cleared of the charges.