As tension with the new state of Israel intensified in January 1949, No 208 Squadron was transferred to the Canal Zone to reinforce the resident fighter squadrons.   Following Israeli incursions into Egypt, the squadron was tasked to carry out reconnaissance sorties along the border.   On January 7, four Spitfires led by Cooper set off for a patrol with instructions not to cross the frontier.   As they turned for home at the end of their reconnaissance, one of the Spitfires was shot down by anti-aircraft fire and the pilot bailed out.   As the other three pilots dived down to look for the descending parachute of their colleague, Israeli Air Force Spitfires appeared and attacked them.   The three 208 Squadron aircraft were hit and Cooper and Flying Officer McElhaw were forced to bail out.   The third pilot was killed.

The RAF Spitfires crashed 10 miles inside Egyptian territory.   Cooper was picked up by Bedouin tribesmen and returned to his base the following day.   The other two pilots were captured and spent a short period in Israeli hands.   It was later claimed by the Israeli pilots (one was a Canadian and a second an American) that they had mistaken the RAF Spitfires for Egyptian aircraft.