By early 1941, tension was beginning to build in the Philippine Islands as Japan began expanding towards Indonesia. In May of 1941, all American dependents in the Philippines were ordered back to the United States as the Philippine Islands began bracing for the Japanese invasion. On December 8, 1941, between 8:30 a.m. and 9:00 a.m., 27 Japanese bombers passed over the City of Baguio on their way to bomb Clark Air Base in Central Luzon. The first bomb to fall on the Philippine Islands exploded at the Military Circle (the Main Gate of Camp John Hay), inflicting the first casualties of war.

Within a month, the Philippines were occupied by the Japanese. Camp John Hay was turned into a concentration camp for American and British citizens. In April of 1942, Camp John Hay became a Japanese Army post. It was built into an important staging area and arsenal, from which the Japanese supplied their soldiers who were fighting in the mountains. They built many tunnels, trenches and pill boxes of re-enforced cement.

In January 1945, General Tomoyuki Yamashita, Commanding Officer of the Japanese Imperial Forces in the Philippines, moved his headquarters from Manila to Baguio in anticipation of the coming invasion of the allied forces. His headquarters was established at the Baguio General Hospital, but was moved to Camp John Hay in order to avoid the staffing and bombing of allied aircrafts. General Yamashita chose the High Commissioner’s House for his residence.

On 27 April 1945, the 33rd Division of the American Army moved into Baguio and continued eastward to Camp John Hay. Like Baguio, Camp John Hay was in ruins. Most of the few buildings that had withstood the bombing were gutted by fire set by retreating Japanese Army. The Officers’ Mess (Main Club) still stood but was badly damaged. The Snyder Hall (Base Gymnasium) withstood the bombings during the war but was destroyed by the July 16, 1990 killer earthquake. The pre-war hospital still occupied the hill overlooking the vegetable garden that had once been a beautiful golf course. The General’s Quarter and Bell Amphitheater had somehow miraculously escaped.