As part of the RAAF's reorganisation following the outbreak of World War II in September 1939, No. 2 Group was formed in Sydney on 20 November, with Cole in command. The group controlled Air Force units in New South Wales. Cole was raised to temporary air commodore in December, and took charge of Central Area Command, which supplanted No. 2 Group, when it was established in the new year. In September 1941, he was sent to North Africa as Officer Commanding No. 235 Wing RAF of the Desert Air Force, where he helped establish a new anti-submarine warfare unit, No. 459 Squadron RAAF. Posted to England with Headquarters No. 11 Group in May 1942, he served as Forward Air Controller of the Dieppe Raid on 19 August, responsible for co-ordinating Allied air cover off the French coast aboard HMS "Calpe". In doing so, he was seriously wounded in the jaw and upper body when German fighters strafed the ship; he required plastic surgery and spent several weeks recuperating. His gallantry during the action earned him the Distinguished Service Order, the announcement being published in a supplement to the "London Gazette" on 2 October 1942. The same month, he was made Air Officer Commanding (AOC) RAF Northern Ireland, with the acting rank of air vice marshal, though the command was described in the official history of Australia in the war as a "backwater".