Wanklyn returned to Gosport in July 1939 and became the first lieutenant and second-in-command of HMS "Otway", part of the 5th Submarine Flotilla, in August 1939. The submarine left Gosport on 24 August 1939 and sailed to Gibraltar to take on fuel and supplies. At the outbreak of war Wanklyn was deployed to Malta on 2 September and then to Alexandria in Egypt on 2 October 1939. Over the course of the Phoney War, "Otway" was in training. On Christmas Day the vessel docked in Marseilles. Wanklyn was ordered to London to receive a new command. He was driven to Paris, where he spent boxing day and then on to Cherbourg, where he sailed for England.