When war began on 3 September 1939 Agar was in command of the "Emerald" and, as in 1914, was directed to Scapa Flow. His ship was soon ordered onto the "Northern Patrol", between the Faroe Islands and Iceland, to intercept any German merchant ships trying to return to their homeland. A second duty was to stop neutral ships and check for contraband headed for Germany. "Emerald" had just returned to Scapa on 1 October 1939 when Agar received "Top Secret" orders to proceed "with all despatch" to Plymouth, England.