On 29 September 1938, Thomas was recalled to active duty, and joined the crew of the battleship . On 13 August 1939, he joined the cruiser , where he was serving when the Second World War broke out. He was promoted to commander on 27 June 1940. After it was sunk by the Italians in the Raid on Souda Bay, he was assigned to HMS "Nile", the Royal Navy shore establishment in Egypt, and served on the staff of the Commander-in-Chief, Mediterranean Fleet. He married a second time on 10 September 1941, to Mary Fedora Douglas-Watson, a pianist and composer. She was the widow of a fellow naval officer, Commander Francis Douglas-Watson, and the daughter of former Australian senator Anthony St Ledger.