Jack Aubrey is a naval officer, a post-captain of experience and capacity. When The Letter of Marque opens he has been struck off the Navy List for a crime he has not committed. With Aubrey is his friend and ship's surgeon Stephen Maturin, who is also an unofficial British intelligence agent.

Maturin has bought for Aubrey his old ship the Surprise, so that the misery of ejection from the service can be palliated by the command of what Aubrey calls a 'private man-of-war' – a letter of marque, a privateer. Together they sail on a voyage which, if successful, might restore Aubrey to the rank, and the raison d'etre, whose loss he so much regrets.