Since the Battle of Little Bighorn in 1876, Miles fought to force resistant Indians all across the nation to give up their traditional ways and accept life on government-controlled reservations. His winter campaign in 1876-77 used force and diplomacy to win the surrender of many of the remnants of the Sioux and Cheyenne Indian party, including Crazy Horse and his followers, that had destroyed Custer's forces in Montana. In 1877, Miles intercepted Chief Joseph and his Nez Perce people as they attempted to flee to Canada and Miles forced them to surrender. A decade later, he played a key role in convincing the last rebellious Apache warrior, Geronimo, to accept confinement on a Florida reservation.
By 1890, Miles had good reason to believe that he had succeeded in bringing an end to the last remnants of Indian resistance in the United States. Therefore, it was with growing alarm and consternation that he received reports of the Ghost Dance movement among his old enemy, the Sioux, on their reservations in South Dakota. Primarily a spiritual movement, many Anglo-Americans felt threatened by the Ghost Dance because it promised that if the Sioux returned to their traditional ways their white oppressors would be eliminated.
As commander of the vast military division of the Missouri, Miles was responsible for any threat posed by the Ghost Dance movement. He reacted by concentrating his troops near the Sioux reservation in South Dakota to maintain control of the situation while simultaneously working to find a peaceful way to diffuse the growing tensions. Unfortunately, Miles' decision to order the arrest of the old Sioux leader, Sitting Bull, only exacerbated the situation when it resulted in the respected chief's death. News of Sitting Bulls' death fanned the fears of some Sioux that the army was preparing to wipe them out in a massive campaign of genocide. Hundreds fled the reservation, and Miles dutifully dispatched troops to bring them back. When the 7th Cavalry under Colonel James Forsyth attempted to disarm one band of Sioux near Wounded Knee on December 19, 1890, a brutal massacre erupted, which left nearly 150 Indians dead, many of them women and children.
Had he actually been present at Wounded Knee that day (Miles commanded these events from his headquarters in Rapid City), the general might well have been able to resolve the confrontation peacefully. Miles viewed Wounded Knee as a foolish and avoidable blunder. Trying to salvage the situation, Miles increased both his military and diplomatic pressures. On January 14, 1891, the Sioux submitted to his authority and returned to their reservation. Nearly a quarter century after the Battle of Little Bighorn, the general had crushed the last significant Indian uprising in American history.