The Surprise , with bow guns blazing, is in close pursuit of the American privateer Franklin in the wine-dark waters of the South Pacific. The chase is interrupted by a submarine volcanic eruption that completely disables the Franklin , with lesser damages to the Surprise . At sunrise, Aubrey sends Reade to take the Franklin ; Maturin and Martin separate the dead from wounded aboard the prize. Jean Dutourd, the owner, is taken aboard Surprise . A wealthy philanthropist, his plan to colonise a South Pacific island, Moahu, was stopped by the appearance of the Surprise , and her support for the successful queen of Moahu in a battle for supremacy on the island. The Franklin took prizes of British ships en route to Moahu, proved by ransomers aboard, seamen taken as security, along with cargoes taken. The American sailing master is dead, killed by shots from the Surprise .
Aubrey finds that Dutourd does not have a letter of marque permitting him to operate the Franklin as a privateer; the sailing master did, but Dutourd is not listed on his muster. Aubrey views Dutourd as a pirate, while Maturin considers him a risk ashore to his mission. Aboard ship, his utopian talk appeals to some of the seamen. They take an American whaler as prize. A British sailor on the whaler tells Aubrey of the Alastor , a privateer turned true pirate, flying the black flag and demanding immediate surrender or death of its victims. In their ultimately successful encounter with the Alastor , Aubrey receives severe wounds to his eye and his leg.
The ships reach Callao, the port for Lima. Maturin's mission begins now, done under cover of Surprise not being a Royal Navy ship, but perceived as a privateer, and she is again in this port with Pullings as her captain, with many prizes in tow. Maturin's goal is to assist the movement for independence of Peru from Spain, with aid from English gold as needed. Father Sam Panda is assigned here, and he proves a useful contact in Maturin's work. Another of Maturin's tasks ashore is to find suitable care for his longtime assistant, Nathaniel Martin, who is too ill for his work at sea. Maturin sees his old friend Dr Geary, surgeon of The Three Graces merchantman, who offers to take Martin home. Martin mistook salt sores (from a period of low fresh water aboard) to be the pox, treating himself with harsh medicines, which in turn made him truly ill. As the hospital in Callao is inadequate, Maturin yields up his patient to Geary.
Maturin meets with Gayongos, revolutionary sympathiser, and departs on a mule into the mountains, to meet with Father Don Jaime O'Higgins. The plan is agreed and will be set in motion in a couple of days. Gayongos reports at the Benedictine monastery that Dutourd is in Lima; Maturin says, let the Inquisition have him. Maturin sends a message to Pullings that he is gone botanizing in the mountains. He meets Eduardo, knowledgeable Inca guide, and the two trek in the higher altitudes. Eduardo receives a message from Gayongos that the revolution has failed before it began. Maturin must flee by land to Chile. Dutourd is arrested as a heretic, but the damage is done. When Aubrey discovers that Dutourd escaped, he sails in a cutter with a few crewmen to Callao to retake Dutourd or to warn Maturin. After many days of hard sailing against the wind, the feared lee shore, they reach the harbour and are taken aboard the Surprise by Captain Pullings barely alive. Aubrey welcomes Sam Panda who updates him on the political situation and the plan to meet with Maturin. Trekking over the Andes Mountains with llamas, Maturin and Eduardo are caught in a viento blanco (blizzard), their lives saved by the shelter Eduardo found, though Maturin loses some toes to frostbite.
Maturin makes his way to Arica with help from Eduardo, and then takes ship to Valparaíso, where Aubrey picks up Maturin and his collections. Maturin informs him of three American China ships sailing from Boston. The Surprise sails to intercept them off Cape Horn but, as she prepares to engage them, is herself fired upon by a thirty-eight gun US frigate and her brig. After a very close encounter with an ice island, the Surprise is again chased until her pursuer sails into a dead end in the ice field. The Surprise sails out, losing her main mast and rudder to a lightning strike. Jury-rigged, her crew spot a ship hull-down on the horizon. The ship, recognized by Maturin as having two rows of cannon, is HMS Berenice under Captain Heneage Dundas, accompanied by her tender, and carries Aubrey's much younger half-brother Philip. Dundas has provisions to repair the ship and pepper for Maturin to preserve his specimens from moths. Dundas has precious news from home, as he visited Ashgrove Cottage before he sailed, seeing Sophia and their children, but not Diana, only her horses. He met Clarissa Oakes there, who is now a widow. Aubrey and Maturin are happily homeward bound.