That year, the United States Penitentiary in Marion, Illinois, on land, opened as the replacement facility for Alcatraz.
Instead, the army switched the focus of its plans for Alcatraz from coastal defense to detention, a task for which it was well suited because of its isolation. The building had been constructed in an excavated pit (creating a dry "moat") to enhance its defensive potential.
In 1867, a brick jailhouse was built (previously inmates had been kept in the basement of the guardhouse), and in 1868, Alcatraz was officially designated a long-term detention facility for military prisoners. After the 1906 San Francisco earthquake, civilian prisoners were transferred to Alcatraz for safe confinement. The first floor was then incorporated as a basement to the new cell block, giving rise to the popular legend of "dungeons" below the main cell block.
Frémont, champion of Manifest Destiny and leader of the Bear Flag Republic, bought the island for $5,000 in the name of the United States government from Francis Temple. Frémont and his heirs sued for compensation during protracted but unsuccessful legal battles that extended into the 1890s.
Frémont had expected a large compensation for his initiative in purchasing and securing Alcatraz Island for the U. Following the acquisition of California by the United States as a result of the Treaty of Guadalupe Hidalgo (1848) which ended the Mexican–American War, and the onset of the California Gold Rush the following year, the U. Army began studying the suitability of Alcatraz Island for the positioning of coastal batteries to protect the approaches to San Francisco Bay. Tower, the United States Army Corps of Engineers began fortifying the island, work which continued until 1858, eventuating in Fortress Alcatraz.
Kennedy ordered the penitentiary closed on March 21, 1963.