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No.680 Squadron was formed from A Flight, No.2 Photographic Reconnaissance Unit at Matariya on 1 February 1943. Equipped with Spitfires, Hurricanes and Beaufighters, it flew photographic reconnaissance missions over enemy bases in North Africa. It moved forward to Tunisia in April 1943 and extended its activities to Sicily and Sardinia, while detachments in Libya and Cyprus kept watch on Greece and Crete.
In June the squadron withdrew its Tunisian-based aircraft to Matariya and concentrated on keeping track of the enemy in the Eastern Mediterranean for a period. In August 1944, a detachment moved to Italy and remained there for a year. After the end of the war other detachments undertook survey work in Iran, Iraq and Palestine. Mosquitoes had been added to the squadron strength in February 1944 and in July 1946 it gave up its Spitfires to become wholly equipped with Mosquitoes. At the same time it moved to Palestine where it was renumbered No.13 Squadron on 1 September 1946.