There were too many Mexican soldiers. Kearny knew he would could not win; he ordered his men to take cover on a small hill. Kearny then sent Carson, a naval lieutenant named Beale, and a Native American scout to get help. The three left on the night of December 8 for San Diego. San Diego was away. Carson and the lieutenant removed their shoes because they made too much noise. They walked barefoot through the desert.
Carson wrote in his "Memoirs": "Finally got through, but had the misfortune to lose our shoes. Had to travel over a country covered with prickly pear and rocks, barefoot." By December 10, Kearny believed help would not arrive. He planned to break through the Mexican lines the next morning. That night, 200 mounted American soldiers arrived in San Pasqual. They swept the area and drove the Mexicans away. Kearny was in San Diego on December 12. Carson went back to Taos after the Mexican–American War to start a ranch.
In 1853, Carson became the United States Indian agent to the Utes. These people lived across northern New Mexico. The Jacarilla Apaches and the Puebloans at the Rio Grande would also come under Carson's watch. Carson's job was to keep the peace between the southwestern tribes, and to hunt down and punish any who committed crimes. Carson was honest and fair as an Indian agent.
Carson came to realize that the hostilities between white Americans and Native Americans were the result of a great decrease in available wild game. This situation forced the Native Americans into raiding American farms, ranches, and herds of cattle. He also knew that the liquor available in towns and villages led the Native Americans into serious trouble. Carson wanted the government to put aside large areas of land far from white settlements. The lands would be called reservations, and were intended for the use of Native Americans only. He thought the Native Americans should be taught agriculture, but it would prove almost impossible to teach nomadic hunters to settle on one piece of land and farm it. He thought his plans would keep these peoples from becoming extinct. Carson resigned as Indian agent with the outbreak of the American Civil War in April 1861. He joined the Union Army to lead the 1st New Mexico Volunteer Infantry.
In April 1861, the American Civil War broke out. Carson left his job as an Indian agent, and joined the Union Army. He was made a lieutenant. He led the 1st New Mexico Volunteer Infantry. He trained the new men. In October 1861, he was made a colonel. The Volunteers fought the Confederate forces at Valverde, New Mexico in February 1862. The Confederates won this battle, but were later defeated.
Once the Confederates were driven from New Mexico, Carson's commander Major James Henry Carleton, turned his attention to the Native Americans. The historian Edwin Sabin writes that this officer had a "psychopathic hatred of the Apaches". Carleton led his forces deep into the Mescalero Apache territory. The Mescaleros were tired of fighting, and put themselves under Carson's protection. Carleton put these Apaches on a remote and lonely reservation east on the Pecos River.
Carson disliked the Apaches. He wrote in a report that the Jicarilla Apaches "were truly the most degraded and troublesome Indians we have in our department ... [W]e daily witness them in a state of intoxication in our plaza." Carson half-heartedly supported Carleton's plans. He was tired. He had suffered an injury two years before that gave him great trouble. He resigned from the Army in February 1863. Carleton refused to accept the resignation because he wanted Carson to lead a campaign against the Navajo.
Carleton had chosen a bleak site on the Pecos River for his reservation. This reservation was called Bosque Redondo (Round Grove). He chose this site for the Apaches and Navajos because it was far from white settlements. He also wanted these Apaches and Navajo to act as a buffer for any aggressive acts committed upon the white settlements from Kiowas and Comanches to the east of Bosque Redondo. He thought as well that the remoteness and desolation of the reservation would discourage white settlement.
The Mescalero Apaches walked 130 miles to the reservation. By March 1863, four hundred Apaches had settled around nearby Fort Sumner. Others had fled west to join fugitive bands of Apaches. By middle summer, many of these people were planting crops and doing other farm work.
On July 7, Carson, with little heart for the Navajo roundup, started the campaign against the tribe. His orders were almost the same as those for the Apache roundup: he was to shoot all males on site, and take the women and children captives. No peace treaties were to be made until all the Navajo were on the reservation.
Carson searched far and wide for the Navajo. He found their homes, fields, animals, and orchards, but the Navajo were experts at disappearing quickly and hiding in their vast lands. The roundup was a great frustration for Carson. He was in his 50s, tired, and ill. By autumn 1863, Carson started to burn the Navajo homes and fields, and remove their animals from the area. The Navaho would starve if this destruction continued. One hundred eighty-eight Navajo surrendered. They were sent to Bosque Redondo. Life at the Bosque had turned grim. Murders occurred. The Apaches and Navajos fought. The water in the Pecos contained minerals that gave people cramps and stomach aches. Residents had to walk about twelve miles to find firewood.
Carson wanted to take a winter break from the campaign. Major Carleton refused. Kit was ordered to invade the Canyon de Chelly. It was here that many Navajos had taken refuge. Historian David Roberts writes, "Carson's sweep through the Canyon de Chelly in the winter of 1863-1864 would prove to be the decisive action in the Campaign."
The Canyon de Chelly was a sacred place for the Navajo. They believed it would now be their strongest sanctuary. Three hundred Navajo took refuge on the canyon rim at a place called Fortress Rock. They resisted Carson's invasion by building rope ladders, bridges, lowering water pots into a stream, and keeping out of sight. These three hundred Navajo survived the invasion. In January 1864, Carson swept through the 35-mile Canyon with his forces. He cut down the thousands of peach trees in the Canyon. Few Navajo were killed or captured. Carson's invasion however proved to the Navajo that the white man could invade their country at any time. Many Navajo surrendered at Fort Canby.
By March 1864, there were 3,000 refuges at Fort Canby. An additional 5,000 arrived in the camp. They were suffering from the intense cold and hunger. Carson asked for supplies to feed and clothe them. The thousands of Navajo were led to Bosque Redondo. Many died along the way. Stragglers in the rear were shot and killed. In Navajo history, this horrific trek is known as The Long Walk. By 1866, reports indicated that Bosque Redondo was a complete failure. Major Carleton was fired. Congress started investigations. In 1868, a treaty was signed, and the Navajo were allowed to return to their homeland. Bosque Redondo was closed.
On November 25, 1864, Carson led his forces against the southwestern tribes at the First Battle of Adobe Walls in the Texas panhandle. Adobe Walls was an abandoned trading post blown up by its inhabitants to prevent a take-over by hostile Native Americans. Combatants at the First Battle were the United States Army and masses of Kiowas, Comanches, and Plains Apaches. It was one of the largest engagements fought on the Great Plains. The Texas State Library and Archives Commission writes: "The result of Adobe Walls was a crushing spiritual defeat for the Indians. It also prompted the U.S. military to take its final actions to crush the Indians once and for all. Within the year, the long war between whites and Indians in Texas would reach its conclusion."