Thus it is understandable that passions flared up on both sides of the conflict. The direct result of these passions was the rise of guerilla warfare. During the period from the mid 1860s all the way through 1890, both the Indians and the white forces committed many atrocities. In 1864 the Cheyennes and Arapahos of southern Colorado sued for peace and made camp by Sand Creek to wait for a response. There they were brutally slaughtered by the Colorado militia, which continued its onslaught, killing women and children, even after the Indians had raised a white flag in surrender. In 1866, the Teton Sioux in Wyoming attacked troops working on the construction of the Bozeman Trail (a road between Wyoming and Montana), killing and mutilating the 80 soldiers at work. Events such as these led to the rise of bitter hatred between the two contending groups, which continuously spilled over into brutality and violence as the prolonged conflict went on.

Not all whites, however, were employed in the direct destruction of the Indians. Many took a more beneficent view of the Plains Indians, seeing it as their duty to Christianize and modernize the "savages" on the reservations. To this end, the Board of Indian Commissioners delegated the task of reform to Protestant leaders. Though cloaked in goodwill, this effort served the more practical purpose of breaking the nomadic tradition of the Indians and making them into permanent and productive members of the reservations. Other attempts were made throughout the late 1800s to "save" the Indians. Richard H. Pratt founded the Carlisle Indian School in Pennsylvania to equip Indians with the skills and culture necessary for integration into white society. However, the school uprooted Indians from their homes and made no pretense of respecting Indian culture. This sort of cultural reeducation assaulted the Indian way of life as viciously as the hunters who had slaughtered the buffalo. The movement to "civilize" the Indians was infused with a sense of cultural superiority. Pratt explained that that goal of the Carlisle School was to "kill the Indian and save the man." Other humanitarians, genuinely concerned about the Indians, suggested that the best thing for them would be to integrate the tribes into white society, instituting concepts like private property and making the Indians less culturally distinct. These concerns were expressed in the 1887 Dawes Severalty Act. The Dawes Act called for the breakup of the reservations and the treatment of Indians as individuals rather than tribes. It provided for the distribution of 160 acres of farmland or 320 acres of grazing land to any Indian who accepted the act's terms, who would then become US citizens in 25 years. While some Indians benefited from the Dawes Act, still others became dependent upon federal aid.

After Indian resistance died out, many did try to adapt to non-Indian ways. Few succeeded completely, and many were emotionally devastated at being forced to abandoned age-old traditions. On reservations, the Plains Indians were almost totally dependent upon the federal government. Indian traditions, social organization, and modes of survival were broken down. By 1900, the Plains Indian population had fallen from almost 250,000 to only slightly more than 100,000. However, the population began to stabilize and slowly rise again, and the traditions of the Plains Indians were maintained as best they could be, considering the situation.

In the period following the Civil War non-Indian settlers pursued a strategy involving a mixture of benevolence, coercion cloaked in legality, and blind violence to change the Indian lifestyle in the name of civilization and progress. Many white Americans felt only contempt toward the Indians, but others viewed themselves as divinely chosen to uplift and Christianize the Indians. Both groups participated equally in the destruction of the Native American culture, however, and the fate of the Indians continues to rest heavy on the American conscience.

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