Jack Aubrey and Doctor Stephen Maturin return home to discover that much has changed in their absence. Jack finds that he has been promoted to Commodore and given a new mission to stamp out the slave trade on the west coast of Africa, while Stephen discovers that his enemy the Lord of Habachtschal is conspiring to bring treason charges against him for his previous conduct as a British spy and for his support of Clarissa Oakes and Padeen Coleman. Stephen must spirit the two out of danger and then join Jack and his new squadron on their mission in Africa. Little do both men know that the Africa mission is a cover for an even more important task of surprising a French fleet that is planning an invasion of Stephen's home country of Ireland.

Jack and Stephen return from the Indian Ocean aboard Jack's ship, the Surprise. They reach home to find that much has changed in their absence. For Jack, the glory of a promotion to Commodore and a new mission to thwart the slave trade on the west coast of Africa, is marred by burgeoning troubles with his wife Sophie. Sophie believes Jack has had an affair with Clarissa Oakes, who Jack and Stephen rescued on a previous adventure and who now lives nearby, caring for Stephen's young daughter Brigid. Jack, in turn, is angered by some of Sophie's decisions in handling his affairs while he is away. The two quarrel while Jack is home and are no longer speaking to one another when Jack's new squadron leaves for the African Coast.

Stephen returns home to find that his wife Diana, unable to bear the burden of their new daughter Brigid, has fled, leaving Stephen a note explaining her actions. Brigid is now in the care of Clarissa Oakes. Stephen soon learns of a plot by Lord Habachtschal to have Stephen arrested for treason. Stephen is forced to take what possessions he can, along with Clarissa Oakes, his daughter Brigid, and his steward Padeen Coleman, all of whom are in danger from the plotting Habachtschal, and join Jack on his journey south.

After leaving Clarissa, Padeen, and Brigid in the care of an aunt in Spain, Stephen and Jack travel to the west coast of Africa. On the way, Jack learns of his secret mission. He is to make a show of engaging the slave runner ships on the west coast, and then double back to intercept a French invasion fleet, that British spy say is planning to land in Stephen's home country of Ireland.

The Commodore's fleet has great success capturing slave ships, though Stephen catches yellow fever and nearly dies. Finally, they turn back toward home and tail the newly formed French fleet to the coast of Ireland, where Jack succeeds in foiling the invasion. Jack mends the rift with his wife Sophie, and Stephen returns to his wife Diana.