From "Daedalus" Kelly moved to become first lieutenant of the 64-gun in March 1810. "Polyphemus" was the flagship of Vice-Admiral Bartholomew Rowley, who died during his posting. Kelly was sent home with the despatches aboard . He captained the 18-gun sloop during the Invasion of Java between August and September 1811, and was promoted to commander on 28 November 1811. He then spent a period on half-pay without active employment, despite petitioning the Admiralty for a posting during the War of 1812 and Lord Exmouth's expedition to Algiers.