Treason's Harbour by Patrick O'Brian

Malta, in 1813, is ostensibly a safe harbour, yet the island is a nest of French spies, and even those in authority are not to be trusted. As Captain Jack Aubrey cools his heels in a Maltese harbour, awaiting repairs to his ship, war rages on. Fearing that hostilities will end before he has any further opportunities for fame and fortune, Aubrey accepts several secret missions, but all is not as it seems.

Will a double agent be the undoing of both Jack Aubrey and his friend, ship's surgeon Stephen Maturin?