During the early days of the war, Lieutenant Parsons worked resupplying American submarines which came into Manila Bay, or relocating supplies to Bataan and Corregidor. As the Japanese army approached Manila at the end of 1941, Parsons spent New Year's Eve destroying what was left of the Navy's supplies in Manila, as well as the contents of the warehouses belonging to his various companies. Although recently promoted to lieutenant commander, he also burned his Navy uniforms as he was not retreating to Bataan with the rest of the American-Filipino forces. Before World War II broke out in the Philippines, Charles Parsons' wife, sons, and his mother-in-law Blanche Jurika had not been evacuated with other military dependents, as the Philippines was their home. In early January, they awoke one day to find a Japanese sentry at the gate to their house, along with a sign stating that the house was now the property of the Imperial Japanese government.