Pope returned to the West as commander of the Department of the Missouri (the nation's second-largest geographical command) during the Grant presidency, and held that command through 1883. He served with distinction in the Apache Wars, including the Red River War relocating Southern Plains tribes to reservations in Oklahoma. General Pope made political enemies in Washington when he recommended that the reservation system would be better administered by the military than the corrupt Indian Bureau. He also engendered controversy by calling for better and more humane treatment of Native Americans, but author Walter Donald Kennedy notes that he also said "It is my purpose to utterly exterminate the Sioux" and planned to make a "final settlement with all these Indians".O.R., Series I, Vol. XIII, p. 686.
