Mineral finds in the West continued to draw large numbers of miners. The U.S. government exacerbated the situation by implementing the Homestead Act and Conscription Act as well as starting construction on the transcontinental railroad during this period, essentially turning the stream of emigrants invading tribal lands into a torrent. The Civil War years saw the greatest numbers of emigrants on the trails that led to Western destinations. Population centers like Denver and Salt Lake City helped to squeeze Indians from one area into the territory of another tribe, also creating a ripple effect of conflict between Indians. The military used tribes against one another, for example allowing the Utes to take Navajo Indians as prisoners and sell them into slavery. This was after the emancipation proclamation has started to rein in slavery back in the East.
It was a time of mass murder on a scale unseen since Pontiac's War a hundred years earlier. The army sought out Indian encampments with a will. Massacres at Bear River and Sand Creek resulted in hundreds of dead, mostly women and children. (There were many smaller such massacres.) The army hung Indians on the flimsiest of evidence. In October of 1863 Col. Robert Livingston set huge prairie fires between Julesburg and the Missouri River in an attempt to create an environment inhospitable to the tribes. It must not have worked well as in January of 1864 in the area between Ft. Kearny and the South Platte River. Julesburg was sacked and burned twice within a year. Stage stations and telegraph stations were raided and small wagon trains became easy targets. Native American leaders experimented with new operational and tactical approaches to fighting. Instead of the traditional small raiding parties, regiment and brigade sized war parties swamped the defenses of the U.S. Army, which counted upon being able to stand off attacks of small parties with small garrisons armed with long-range weapons. Crazy Horse first tried the ambuscade technique, that resulted in the destruction of Lt. Fetterman's command, two years earlier at Platte Bridge Station. The failed attempt in 1865 led to a successful springing of a similar trap in 1867.
As the war in the East ended, huge numbers of soldiers were freed up to serve in the ongoing war in the West. Those pesky laws of logistics came into play again and as long as the post war surge was in play the war cooled down. In 1867, after most troops had been mustered out, war on a smaller scale returned. It was called Red Clouds War and it was a clear loss for the U.S. Army.