The book continues the story of Jack Aubrey's exploits during the War of 1812. Aubrey reports to his commander-in-chief at Gibraltar, who sends him and HMS Surprise to intercept the American frigate USS Norfolk which plans to attack British whalers in the South Seas. Jack makes all haste to have the Surprise victualled as quickly as possible and recruits a new master, a Mr Allen. Not only is he an excellent seaman but he also has an in-depth knowledge of whalers, having sailed previously with Colnett on a semi exploration-whaling expedition to the South Atlantic. Stephen Maturin also persuades Jack to take Mr Martin along with them, a clergyman who Jack approves of and who is unhappy with his current ship.
Maturin receives disturbing news from his intelligence-chief in London, Sir Joseph Blaine, which tends to confirm his suspicions of treason and infiltration by the French. He also hears from his wife, who has heard rumours of the infidelity he pretended in Valetta, Malta with the red-haired Mrs Fielding for intelligence reasons. He sends a letter to reassure her via Andrew Wray, unaware of the latter's role as a French agent.
The Surprise encounters many setbacks, suffering delays in Brazil from a lightening-struck prow before they round Cape Horn into the Pacific Ocean to locate the Norfolk, which has captured and burnt several whalers. The British, having nearly been shipwrecked by the tail of a typhoon, finally discover the Norfolk wrecked on a reef by the same typhoon and her crew encamped on an island. Aubrey, Mr Martin and some of the crew take Stephen ashore as he has fallen unconscious from an accident and needs to be on land to recover. However, although Stephen makes a recovery, another heavy storm blows the Surprise away and they are left stranded. Relations between the two marooned groups deteriorate rapidly, particularly after Jack announces to the American Captain Palmer that he will have to take his crew prisoner. Some of them are from the Hermione that mutinied in the West Indies and they know they will be hanged if caught. The situation reaches a crisis point after Jack orders to Surprises to extend their boat so they can sail away, pushing them particularly hard when he sees an American whaler on the horizon. The Norfolks sabotage the boat after spotting the same whaler but it is at this point that they see her strike her colours, having been pursued through a gap in the reef by the Surprise.
A sub-plot in the book is the illict affair between the sweet singing but otherwise untalented Hollom, a passed midshipman but too old to become a lieutenant, and the pretty wife brought aboard by the sexually impotent gunner, Horner. Hollom is considered a Jonah by the crew - someone who brings bad luck to the ship - and the two lovers are beaten to death by the ferocious, brutal and jealous husband on an island whilst the Surprise is being provisioned. Horner himself sinks into a black despair and is discovered hanging in his cabin.[[Cate