Even while they were fighting the Confederacy, Union forces had another opponent to contend with: American Indian tribes in the Southwest. These battles with Indians—including the Navajo war—had a direct effect on the War Between the States.
The confrontation between the Navajo and the U.S. government had been brewing ever since the end of the Mexican-American War in 1848. As part of the treaty that ended that conflict, Mexico turned over a large swath of land in what are now the Southwest states, which included Navajo territories.
A decade of small conflicts and raiding on both sides led to total war in 1860, when about 1,000 Navajos attacked Fort Defiance in modern-day Arizona. They nearly took the fort but ultimately lost to American troops, who were aided by other nearby tribes such as the Ute and Zuni tribes, traditional enemies of the Navajo.
The conflict between the Navajo and the States might have been resolved quickly, but along came the Civil War. Union soldiers left the New Mexico territory to battle Confederate troops in Texas, leaving a vacuum for the Navajo and other local tribes to step up raids. By 1863, with the Confederate forces routed in Texas, the federal government once again focused on the Navajo. Col. Christopher "Kit" Carson was charged with the task of driving the native Indian population into submission.
After arriving at Fort Defiance, he proceeded to burn crops and villages and capture livestock. Deprived of these commodities and faced with the impending winter, many Navajos surrendered. By 1864, about 8,000 members of the tribe were forced to undertake the "Long Walk" to a reservation in New Mexico, many perishing along the way.