In 1896, with the Mescalero Apache settled on the nearby reservation & the surrounding area bustling with new communities, the Fort was abandoned by the Army and closed. In 1899 the US Public Health Service acquired the Fort as a tuberculosis hospital for the Merchant Marine. Selected for its healthful climate, it served some 5,000 sailor patients between 1899 and 1953 - 1,500 of whom are buried in the Maritime Cemetery near the Fort. The patients lived in specially constructed tents, for fresh air and sunshine were the only known cures for tuberculosis. During this time, many new buildings were constructed including a hospital, stables, new living quarters, and literally hundreds of tent-houses for the patients. The hospital was fairly self-sufficient, establishing a large farm on the nearby grounds with patients serving in the fields, as well as recreational activities like a golf course for the doctors, baseball fields and a theater for the resident workers.
The Merchant Marine Cemetery grew to include veterans of other services as well as Merchant Marines, making it a place for current visitors to the site to engage in contemplative visitation. On Veteran's Day, 2015, Governor Martinez declared this cemetery as the Fort Stanton State Veterans Cemetery. Through the efforts of U.S. senators Heinrich and Udall of New Mexico, the VA gave 5 million dollars to the State of New Mexico to expand the cemetery onto an additional 13 acres. Of course archaeological clearance had to be done and structures were excavated before construction could begin.