During World War II the need for troops in the Pacific far exceeded prior needs. The facilities on Angel Island were expanded and further processing was done at Fort Mason in San Francisco. Prior to the war the infrastructure had been expanded, including building the Army ferry USAT General Frank M. Coxe, which transported troops to and from Angel Island on a regular schedule. Fort McDowell was used as a detention station for Japanese, German and Italian immigrant residents of Hawaii arrested as potential fifth columnnists (despite a lack of supporting evidence or access to due process). These internees were later transferred to inland Department of Justice and Army camps. Japanese and German POWs were also held on the island, supplanting immigration needs, which were curtailed during the war years.
The army decommissioned the military post in 1947. In 1954 a Nike missile station was installed on the island. The missile magazines were constructed above Point Blunt on the island's southeast corner, and the top of Mount Ida (now Mount Caroline Livermore) was flattened and the associated radar and tracking station (IFC) was installed there. The missiles were removed in 1962, when the military finally left the island. The missile launch pad still exists, but the station atop Mount Caroline Livermore was completely removed and the mountaintop was later restored to its original contours.