Indian reservations of one sort or another have been a part of Indian affairs since the colonial days. In the nineteenth century, as the United States expanded west, an evolving reservation system developed from an ad hoc assortment of temporary measures in the territories into a continental system for neutralizing “the Indian problem” by isolating and containing native populations. The reservation system evolved steadily from the 1840s, through the Civil War, and into the 1880s and 1890s. A vision of a permanent Indian country – the vision that had justified many of the arguments for removal – collapsed as the United States absorbed Western areas through the 1840s. Commissioner William Medill's vision of two giant reservations in the West, with settlements and railroads to the West Coast running between, drove much of the government's efforts in the late 1840s and 1850s. But even that plan rapidly had to be revised, as administrators in diverse contexts from the Indian Territory, to the Dakota Plains, to Texas, California, and Oregon confronted different environments and unique populations.

The Bureau of Indian Affairs steadily maintained its status as the preferred institutional vehicle for administering Indian policy, despite criticisms of the removal policy. The military played an important role, but the nation's officials never committed to a Western policy dominated and run by the military. As in years past, the cost, risk, and violent consequences of military action dissuaded leaders from making the military more than a temporary expedient or a consistent backup to the civilian service.