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The traditional Navajo homeland is called, in the Navajo language, Dinétah and included land within the borders of the four sacred mountains, from northeastern Arizona through western New Mexico, including Canyon de Chelly, where they had houses and raised livestock. There was a long historical pattern in the Southwest of groups or bands raiding and trading with each other. This included Navajo, Spanish, Mexican, Apache, Comanche, Ute, and later (1846) the new settlers (Americans). Events in the period between 1846 and 1863 included a cycle of treaties, raids and counter-raids by the Army, the Navajo and a civilian militia, with civilian speculators often on the fringe. Most of the militia involved were long time enemies of the Navajo, Spanish descendants from northern New Mexico where Spain had established several settlements in the 17th century.

Hostilities between the Navajo and Spanish colonists began in the late 1600s. They escalated between the Americans and Navajos following the scalping of the respected Navajo leader Narbona in 1849. In August 1851, the U.S. government established Fort Defiance (near present-day Window Rock, Arizona) and Fort Wingate (originally Fort Fauntleroy near Gallup, New Mexico). The Bonneville Treaty of 1858 reduced the extent of Navajo land. There were also treaties negotiated and signed in 1849, 1858 and 1861, but they all failed.

There are many examples of friction between these groups between 1846 and 1863. They include the murder of a personal servant of Major Brooks, commander of Fort Defiance, for an alleged rape of a Navajo in July 1858. There was an attack on Fort Defiance by about 1,000 Navajo warriors under the leadership of Manuelito and Barboncito on April 30, 1860, Navajos were angry that the Army did not bring in feed for their many animals and took the best grazing land, which was not covered by their treaty. A new treaty was signed around February 15, 1861, to pacify the Navajo, but two of their four sacred mountains were lost to them, as well as about one third of their traditionally held land. In March, a company of 52 citizens led by Jose Manuel Sanchez drove off a bunch of Navajo horses, but Captain Wingate followed the trail and recovered the horses for the Navajo, who had killed Sanchez. Another group of citizens ravaged Navajo rancherias in the vicinity of Beautiful Mountain. Also during this time, a party of Mexicans and Pueblo Indians captured 12 Navajo in a raid, and three were brought in.

On Aug. 9, a Spaniard named Lt. Col. Manuel Antonio Chaves of the New Mexico Volunteer Militia took command of a garrison of three companies numbering 7 officers and 203 men at Ft. Fauntleroy. Chaves was later accused of being prodigal in dispensing his post’s supplies to the 1000 or more Navajos that had remained close to the fort, and was remarkably lax in maintaining discipline. Horse races began on Sept. 10 and continued into the late afternoon of Sept. 13. Col. Chaves permitted Post Sutler A. W. Kavanaugh to supply liquor freely to the Navajos. There was a dispute about which horse won a race. A shot rang out, followed by a fusillade. Almost immediately 200 well-armed and mounted Navajo advanced towards the Guard, shooting at the men. They were fired upon by the soldiers, and scattered leaving 12 dead bodies and forty prisoners. On hearing this, Gen. Canby demanded a full report from Chaves, who did not comply. Col. Canby sent Captain Andrew W. Evans to the fort, named Fort Lyon since Sept. 25, and he took command. Manuel Chaves, suspended from command, was confined to the limits of Albuquerque pending court martial. Four years later, a Congressional committee investigating the conditions at Ft. Sumner, heard testimony that the Ft. Fauntleroy episode of the horse race resulted in mountain howitzers being fired at the Indians, resulting in 20 or 30 being killed. A few days later another soldier testified that on the day of the horse race, he saw a soldier murdering two little children and a woman and tried to stop him, but was prevented by a Lt. Ortiz. He also said 12 or 15 Navajo were killed. The rest scattered and the peace that had been hoped for was impossible. In February 1861, Manuel Chaves of the New Mexico Volunteer Militia took the field with 400 men and ransacked Navajo land, basically without federal authority.

With Confederate troops moving into southern New Mexico, Col. Canby sent Agent John Ward into Navajo lands to persuade any who might be friendly to move to a central encampment near the village of Cubero where they would be offered the protection of the government. Ward was also instructed to warn all Navajos who refused to come in that they would be treated as enemies; he was partly successful. Captain Evans was overseeing the abandonment of Ft. Lyon and had been told that the new policy would be that the Navajo had to colonize in settlements or pueblos, mentioning the region of the Little Colorado west of Zuni as possibly an ideal place. In November, some Navajo were raiding again. On Dec. 1, Col. Canby wrote to his superior in St. Louis that “there is no choice between their absolute extermination or their removal and colonization at points so remote as to isolate them entirely from the inhabitants of the Territory.”

By 1862, the Union Army had pushed the Confederates down the Rio Grande. The United States government again turned its attention to the Navajos, determined to eliminate Navajo raiding and raids on the Navajo.

James H. Carleton was ordered to relieve Canby as the Commander for the New Mexico Military Department in September 1862. Carleton gave the orders to Kit Carson to proceed to Navajo territory and to receive the Navajo surrender on July 20, 1863. When no Navajos showed up, Carson and another officer entered Navajo territory in an attempt to persuade Navajos to surrender, and used a scorched earth campaign to starve the Navajo out of their traditional homeland and force them to surrender. He was partly successful by early 1863, when thousands of Navajo began surrendering to the Army.

Some Navajos evaded and refused to surrender to the U. S. Army. These groups scattered to Navajo Mountain, the Grand Canyon, the territory of the Chiricahua Apache, and to parts of Utah.