This is the 17th of Patrick O'Brian's novels about the adventures of Captain Jack Aubrey of the British Navy, and his friend, Stephen Maturin, the ship's surgeon and secret intelligence agent. Aubrey is a large, hearty, cheerful man who loves music and astronomy, and whose fortunes wax and wane as O'Brian follows him through numerous engagements and exploits around the world, roughly from 1800 to 1815. (While the early books in this series place Aubrey in some of the actual sea battles of the British war against Napoleon, "real time" gets suspended in the later novels.)

Maturin is small, dark, and secretive; of Irish and Basque descent; and a Roman Catholic. Nonetheless, he hates Napoleon so much that he becomes an agent for the British, working under the intelligence chief, Sir Joseph Blaine. Maturin is also a famous physician and naturalist, and he plays the cello to Aubrey's violin. The two men are the closest of friends, despite their many differences; in fact, this series of novels is the story of two complex and engaging characters and their years of friendship, as much as it is a series of sea yarns and adventures.

In The Commodore, Aubrey and Maturin have returned to England after a protracted trip around the world that occupied the previous four novels. Aubrey happily spends time with his wife and children, but Maturin discovers that his wife, Diana, has disappeared and his young daughter appears to be autistic.

Shortly, Aubrey receives orders to lead a squadron of ships to the west African coast, where he is to harass the slavers and, on the return voyage, to engage a French squadron being sent (secretly) to attack Ireland. Maturin joins the squadron after carrying his daughter to safety in Spain. They successfully knock off some slaving ships and terrorize the Coast of Guinea, before hurrying back to the southwestern coast of Ireland where they catch up with the French ships and defeat them.