During the Second World War, Scott served in the Royal Navy Volunteer Reserve. As a Sub-Lieutenant, during the failed evacuation of the 51st Highland Division he was the British Naval officer sent ashore at Saint-Valery-en-Caux in the early hours of 11 June 1940 to evacuate some of the wounded. This was the last evacuation of British troops from the port area of St Valery that was not disrupted by enemy fire.[6]
Then he served in destroyers in the North Atlantic but later moved to commanding the First (and only) Squadron of Steam Gun Boats against German E-boats in the English Channel.[7] He was awarded the Distinguished Service Cross for bravery.