In April 1942, Jeffrey was appointed to establish and command No. 2 Operational Training Unit (No. 2 OTU). Initially based at Port Pirie, South Australia, the unit relocated to Mildura, Victoria, the following month, training pilots for combat in such aircraft as Kittyhawks, CAC Boomerangs and Supermarine Spitfires. Its instructors under Jeffrey included aces Clive Caldwell and Wilf Arthur. Jeffrey married Colleen Crozier at Toorak Presbyterian Church in Melbourne on 14 May; his best man was fellow ace and No. 3 Squadron veteran Alan Rawlinson. The couple had two sons. In August 1943, Jeffrey took charge of No. 5 Fighter Sector Headquarters, based in Darwin, Northern Territory. On 25 September, he took over from Caldwell as Officer Commanding No. 1 (Fighter) Wing, comprising three Spitfire squadrons whose role was to defend North-Western Area (NWA) from air attack. By this time, Japanese raids had declined in strength and frequency, and Allied forces in the NWA shifted from a defensive posture to assaulting Japanese positions in the Dutch East Indies and Western New Guinea. No. 1 Wing intercepted some raiders in late September but none came in October; the last Japanese attack on northern Australia took place on 12 November. Jeffrey was promoted to temporary group captain in December.