However, as Axis raids on Malta intensified in 1942, particularly targeting urban areas, the construction of St. Peter's Galleries was temporarily halted. The tunnelers, initially assigned to this project, were redirected to build civilian air raid shelters across the island. By the end of 1942, approximately 30 cubic miles of underground shelters had been completed, providing a minimum space of 3x3 feet for each person, including the troops stationed on the island. During this time, Royal Engineers miners also worked on various underground military facilities such as stores, workshops, troop accommodation, and operation rooms.
 

As the Allies secured North Africa, the decision to invade Italy through Sicily was made at the Casablanca conference. Malta was chosen as the headquarters and primary launching point for the Allied invasion force. This decision necessitated extensive infrastructural and logistical preparations, with the Royal Engineers' Tunnellers once again playing a crucial role. In June 1943, work on St. Peter's Galleries resumed, but in August of the same year, Sicily fell to the Allies, and on September 8, Italy surrendered. In October, Malta's siege was lifted, rendering the completion of the new Combined War HQ unnecessary. All construction ceased, and the site was sealed and abandoned, leaving everything inside.
 

In 2009, during the restoration of the nearby Lascaris War Rooms, these tunnels were accidentally rediscovered. Over the next few years, they were adapted for public visits, enhancing the War HQ & Lascaris War Rooms experience for visitors.