As settlement of the northern Great Plains increased, United States military presence also increased to protect settlers. With the establishment of the Dakota Territory in 1861, trespassing on traditional Native American land continued and the establishment of military forts increased. Between 1862 and 1872, the army built eight forts to protect the settlers and people traveling west, to protect the workers building the railroads, and to control the Native Americans, primarily the Dakota.

In 1876, from Fort Abraham Lincoln (five miles south of present day Mandan, North Dakota) on the banks of the Missouri, Colonel George A. Custer lead the pursuit of Sitting Bull which ended with the Battle of Little Big Horn. The increased presence of, and harassment by, the military, coupled with an endless string of broken treaties with the Native Americans, led to the military defeat of Native Americans and to their confinement on reservations.