Keys arrived at what would become his ranch in 1910 and gradually took over the properties that Jim McHaney's gang had previously occupied — including the Desert Queen Mine, which he operated from 1917 onward. He befriended Death Valley Scotty, the eccentric prospector and showman who was himself a fixture of desert California. He built an adobe barn, a schoolhouse, a tack shed, and a machine shed. He raised children on the ranch. His wife Frances joined him and the family grew around the infrastructure Keys was constantly extending and improving. The ranch became a working compound in the high desert, organized around water sources, mining operations, and the cattle that ranged across the public land surrounding it.

On May 11, 1943, Bill Keys shot and killed Worth Bagley near the Wall Street Mill, a gold ore-crushing facility Keys had built in the park. The two men had a longstanding dispute over a road that ran through the area, and their confrontation that day turned fatal. Keys was charged with murder, but the jury convicted him of manslaughter — he was 63 years old at the time — and he was sentenced to ten years at San Quentin State Prison. He served five years before being paroled in 1950. A marker Keys himself placed at the site of the shooting read, in characteristically direct language: "Here is where Worth Bagley bit the dust at the hand of W. F. Keys, May 11, 1943."

The author Erle Stanley Gardner was already famous as the creator of Perry Mason, the defense attorney protagonist of his enormously popular mystery novels, when he took an interest in Keys's case. Gardner believed that Keys had acted in self-defense and that the conviction was unjust. He organized an effort to win Keys a pardon, working through the legal and political channels available to a man of his celebrity and resources. In 1956, Governor Goodwin Knight granted the pardon, and Keys was officially cleared. Gardner's intervention on behalf of a desert rancher he had come to know is one of the stranger footnotes in California criminal history — the creator of America's most famous fictional defense attorney winning a real acquittal for a man who had spent years in prison.

Bill Keys died in 1969 at the age of 89, having outlived most of the people who had known the Joshua Tree desert before the national monument and park designations transformed it. His ranch became part of Joshua Tree National Park and is now managed as a historic site. Ranger-led tours run from October through May, covering the adobe structures, the schoolhouse, and the equipment that Keys accumulated over six decades of desert life. The tours require advance booking — the site is not open for casual visits — which gives it the quality of a place accessed deliberately rather than accidentally, appropriate for a ranch that itself required deliberate commitment to reach and maintain. Keys's story, told through the buildings he built and the landscape he inhabited, is one of the most complete records available of what early settlement in the Mojave actually looked like.