The Stronghold Unit is co-managed with the Oglala Lakota tribe and includes sites of 1890s Ghost Dances, a former United States Air Force bomb and gunnery range, and Red Shirt Table the park's highest point at .
The next great change came toward the end of the 19th century as homesteaders moved into South Dakota. The U.S. government stripped Native Americans of much of their territory and forced them to live on reservations. In the fall and early winter of 1890, thousands of Native American followers, including many Oglala Sioux, became followers of the Indian prophet Wovoka. His vision called for the native people to dance the Ghost Dance and wear Ghost Shirts, which would be impervious to bullets. Wovoka had predicted that the white man would vanish and their hunting grounds would be restored. One of the last known Ghost Dances was conducted on Stronghold Table in the South Unit of Badlands National Park. As winter closed in, the ghost dancers returned to Pine Ridge Agency. The climax of the struggle came in late December, 1890. Headed south from the Cheyenne River, a band of Minneconjou Sioux crossed a pass in the Badlands Wall. Pursued by units of the U.S. Army, they were seeking refuge in the Pine Ridge Reservation. The band, led by Chief Big Foot, was finally overtaken by the soldiers near Wounded Knee Creek in the Reservation and ordered to camp there overnight. The troops attempted to disarm Big Foot's band the next morning. Gunfire erupted. Before it was over, nearly two hundred Indians and thirty soldiers lay dead. The massacre at Wounded Knee was the last major clash between Plains Indians and the U.S. military until the advent of the American Indian Movement in the 1970s, most notably in the 1973 standoff at Wounded Knee, South Dakota.
Wounded Knee is not within the boundaries of Badlands National Park. It is located approximately south of the park on Pine Ridge Reservation. The U.S. government and the Oglala Lakota Nation have agreed that this is a story to be told by the Oglala of Pine Ridge and Minneconjou of Standing Rock Reservation. The interpretation of the site and its tragic events are held as the primary responsibility of these survivors.
In 1846, Prout published a paper about the jaw in the American Journal of Science in which he stated that it had come from a creature he called a Paleotherium. Shortly after the publication, the White River Badlands became popular fossil hunting grounds and, within a couple of decades, numerous new fossil species had been discovered in the White River Badlands. In 1849, Dr. Joseph Leidy, published a paper on an Oligocene camel and renamed Prout's Paleotherium, Titanotherium prouti. By 1854 when he published a series of papers about North American fossils, 84 distinct species had been discovered in North America - 77 of which were found in the White River Badlands. In 1870 a Yale professor, O. C. Marsh, visited the region and developed more refined methods of extracting and reassembling fossils into nearly complete skeletons. From 1899 to today, the South Dakota School of Mines has sent people almost every year and remains one of the most active research institutions working in the White River Badlands. Throughout the late 1800s and continuing today, scientists and institutions from all over the world have benefited from the fossil resources of the White River Badlands. The White River Badlands have developed an international reputation as a fossil-rich area. They contain the richest deposits of Oligocene mammals known, providing a brief glimpse of life in this area 33 million years ago.
As a part of the war effort, the U.S. Air Force (USAF) took possession of of land on the Pine Ridge Reservation, home of the Oglala Sioux people, for a gunnery range. Included in this range was from then Badlands National Monument. This land was used extensively from 1942 through 1945 as air-to-air and air-to-ground gunnery ranges. Precision and demolition bombing exercises were also quite common. After the war, portions of the bombing range were used as an artillery range by the South Dakota National Guard. In 1968, most of the range was declared excess property by the USAF. are retained by the USAF but are no longer used.
Firing took place within most of the present day Stronghold District. Land was bought or leased from individual landowners and the Tribe in order to clear the area of human occupation. Old car bodies and 55 gallon drums painted bright yellow were used as targets. Bulls-eyes across were plowed into the ground and used as targets by bombardier bombing flights. Small automatic aircraft called "drones" and by screens dragged behind planes served as mobile targets. Today, the ground is littered with discarded bullet shells and unexploded ordnance.
For safety, 125 families were relocated from their farms and ranches in the 1940s. Those that remained nearby recall times when they had to dive under tractors while out cutting hay to avoid shells dropped by planes miles outside of the boundary. In the town of Interior, both a church and the building housing the current post office received six inch (152 mm) shells through the roof. Pilots in practice, operating out of Ellsworth Air Force Base near Rapid City, found it a challenge to determine the exact boundaries of the range. Fortunately, there were no civilian casualties. However, at least a dozen members of flight crews lost their lives in plane crashes.