With the coming of World War II, Alger joined the United States Army, assigned to Squadron 5 at the Army Air Corps Advanced Flying School at Kelly Field in San Antonio, Texas. He flew bombers and attained the rank of captain, claiming to be among the first American troops in Japan after the conclusion of the war in August 1945. He received the Distinguished Flying Cross. On returning to civilian life, RCA refused to rehire him on the grounds that he had been out of television production for too long.