Having survived a long and desperate adventure in the Great South Sea, Captain Jack Aubrey and Stephen Maturin return to England to very different circumstances. For Jack it is a happy homecoming, at least initially, but for Stephen disastrous: his little daughter appears to be autistic, incapable of speech or contact, while his wife, Diana, unable to bear this situation, has disappeared, her house being looked after by the widowed Clarissa Oakes.

Much of The Commodore takes place on land, in sitting rooms and drafty castles, but the roar of the great guns is never far from our hearing. Aubrey and Maturin are sent on a bizarre decoy mission to the fever-ridden lagoons of the Gulf of Guinea to suppress the slave trade, but their ultimate destination is Ireland.

There the French are mounting an invasion that will test Aubrey's seamanship and Maturin's resourcefulness as a secret intelligence agent, and the climax of the story is one of those grand and thrilling fleet actions on which the supremacy of the British Navy was founded.