In June 1943, 2nd Lt. Thompson reported for duty aboard the USS Nashville as Junior Officer of the Marine Detachment. In 1944 he relieved Captain Bill Bonner as commanding officer of the detachment. He served in this role until VJ Day, 1945. The Nashville was General Douglas MacArthur's flagship, supporting his activities in the Pacific, including the Leyte landings in the Philippines. On December 13, 1944, the ship suffered a kamikaze attack.