William Babbington is a in Jack Aubrey's first command, HMS Sophie. As a midshipman, Babbington has an almost insatiable lust for the fairer sex. Stephen Maturin notes that Babbington's stunted growth is likely the result of his frequent encounters, at an early age, with poxed ladies of the evening. Babbington later is made a commander, and then a post captain, both because of his natural ability (augmented by having been trained by Aubrey), and because he has influential relations who control several seats in Parliament. As a Commander of the ship in which Maturin and Diana travel back from Paris, he solemnises their marriage. Babbington himself later falls in love with Admiral Harte's daughter, inconveniently married to the traitorous Andrew Wray.
Babbington was a young, but sexually precocious, midshipman aboard the brig HMS Sophie, Aubrey’s first command. Babbington followed Aubrey as a midshipman into HMS Polychrest and HMS Surprise; in the latter ship, Aubrey appointed Babbington as an acting lieutenant (1805), the promotion later being made permanent after the ship's arrival in India. Babbington returned to serve under Aubrey's direct command as a lieutenant in HMS Leopard (1812), loyally staying with Aubrey when the ship seemed on the verge of sinking after a collision with an iceberg. Babbington accompanied Aubrey on HMS LaFleche as passengers on a voyage intended to return them to England, but LaFleche burned in an accident, resulting in Aubrey, Babbington, and others adrift in a small boat in the South Atlantic. They were rescued by [[HMS Java in time to take part in that ship's disastrous encounter with the USS Constitution. As a prisoner of the American Navy, Babbington was repatriated to England for exchange.
After being repatriated to Endland, Babbington was promoted to commander in HMS Sylphide and then given command of HMS Oedipus, a cartel ship assigned to make Channel crossings between England and France. In that role, Babbington again encountered Jack Aubrey, in company with Stephen Maturin and Diana Villiers, escaping from French custody. During the voyage across the Channel to England, Babbington in his capacity as ship's captain performs a marriage ceremony for Stephen and Diana.
Babbington was given the sloop HMS Dyrad and sailed in the Mediterranean. He encountered Jack Aubrey, by this time captain of HMS Worcester, while narrowly escaping death at the hands of the French in an ambush at the port of Medina. Some years later, Babbington again encountered Aubrey as commander of the sloop HMS Tartarus in the English Channel, where he rendered crucial aid to Aubrey in a cutting out action intended to bolster Aubrey's chances for reinstatement to the Navy List, by helping capture and tow, the french frigate , two gunboats, and two merchantmen. Aubrey had been reluctant to ask Babbington’s assistance out of concern that this could harm Babbington’s prospects for promotion to post captain, but was relieved to find that Babbington had already been promised promotion to that rank because of his family connections (this political influence notwithstanding, Babbington had consistently shown himself to be a brave capable sea officer on numerous occasions).