At the outbreak of World War II, Hely was attached to the operations room at RAF Coastal Command. On his return to Australia in January 1940, he was appointed Staff Officer Plans at RAAF Headquarters, Melbourne. In October, he joined the Deputy Chief of the Air Staff, Air Vice Marshal Bill Bostock, as a delegate to a defence conference in Singapore. The Australian contingent found the local forces ill-prepared for an attack by the Japanese and recommended significant increases in air capability, both in Australia and in the Pacific Islands, to meet the threat. Hely was promoted to temporary wing commander the following January, and was the ranking Air Force delegate at a series of staff talks in Batavia and Singapore regarding the defence of the Dutch East Indies. He became Director of Operations at RAAF Headquarters in August. His promotion to acting group captain was announced on 17 February 1942. Two days later, the Japanese bombed Darwin, Northern Territory; Hely circulated a memo early the next month to all commands on the lessons learnt from the raid. He was posted to Darwin in May to join North-Western Area headquarters as senior air staff officer, and was granted the temporary rank of group captain in January 1943. Hely returned to RAAF Headquarters in March to become Director of Air Staff Plans.