Emery was commissioned as an Army officer immediately on the outbreak of war, on 12 September 1939. There was no Intelligence Corps at the time, so Emery was commissioned into the General List as a 2nd Lt. (108571). His considerable local knowledge and practical experience was invaluable to those preparing the defence of
Egypt against a potential attack from Italian forces to the West and to the South and he was quickly directed to the intelligence desk at General Headquarters (GHQ),
British Troops in Egypt, in
Cairo. An early preoccupation was to ensure the quantity and quality of mapping to be issued to the mobilised units that were pouring into the kingdom from all quarters of the Empire: the going for vehicles needed to be noted, water-sources, newly installed enemy defences, etc. Emery's training as a draughtsman was a great asset; his work-colleagues at this time included the future general
Victor Paley. By 1942, Emery was a War Substantive (WS) captain, but was serving in the rank of Major. His contribution to the success at Alamein was rewarded with a
Mention in Despatches (MiD). At the end of the North African campaign, with the successful landing of Allied troops on mainland Italy, Emery was further recognised with the award of a military MBE, in 1943. In addition, Emery was later promoted to temporary Lt.Col., on taking command of his branch. After six years, Lt.Col. Emery, MBE, was released from service on 27 November 1945, and his wartime rank was given formal confirmation. Though not unique, his record was nevertheless impressive for an officer with no previous military experience (PME) who was commissioned after the start of the war: to be promoted from Second Lieutenant to Lieutenant-Colonel, and to be awarded an honour in addition, indicated an exceptional contribution that was notable in itself. In the immediate aftermath of the war, with many archaeological sites still off-limits, Emery accepted a diplomatic post with the British embassy in Cairo. Starting as an Attaché in 1947, he rose to the rank of First Secretary, until his resignation in 1951 to accept an academic role in London. ==Professor of Egyptology==