The land was again appropriated by the United States Navy at the onset of World War II and became one of the major shipyards of the west coast. The Navy reacquired it in November 1941, later renaming it Hunters Point Naval Shipyard, then Treasure Island Naval Station Hunters Point Annex, and operated the yard until 1974, when it leased most of it to a commercial ship repair company. Many workers, including African Americans, moved into the area to work at this shipyard and other wartime related industries in the area. After the war, the area remained a naval base and commercial shipyard, as many blue collar industries moved here. The Navy closed the shipyard and Naval base in 1994 as part of the Base Realignment and Closure (BRAC). The BRAC program manages the majority of the site to this day.
The key missile components of the first atomic bomb were loaded onto the USS Indianapolis in July 1945 at Hunters Point for transfer to Tinian.
As in most industrial zones of the era, Hunter's Point has had a succession of coal and oil fired power generation facilities, and these have left a legacy of pollution, both from smokestack effluvients and leftover byproducts that were dumped in the vicinity. The base was entirely closed in 1994, although it continues to receive attention due to the large amounts of toxic waste remaining to be cleaned up.
After World War II and until 1969, the Hunters Point shipyard was the site of the Naval Radiological Defense Laboratory, the US military's largest facility for applied nuclear research, which has left many areas of the shipyard radioactively contaminated.
The Hunters Point shipyard has recently been targeted as a possible location for a new San Francisco 49ers stadium.