Colonel Edward R. S. Canby, Union commander of the Department of New Mexico, soon learned of the invasion plans. By 1862, Canby had 4,000 troops at the ready. Sibley began his move up the Rio Grande with 3,000 riflemen. The first major battle took place at Valverde near Fort Craig, 100 miles south of Albuquerque, on February 21, 1862. The Confederates won the battle and Sibley decided to press on to Albuquerque.
Sibley sent Major Charles Pyron and his Fifth Texas Regiment ahead of the main Confederate force to capture the unprotected capital of Santa Fe. On March 13, the Confederate flag flew over the Palace of the Governors. Pyron's Texans then made their way up the Santa Fe Trail toward Fort Union and camped at Johnson's Ranch in Apache Canyon.
On the morning of March 26 Union Major John M. Chivington set out on a reconnaissance mission to find the location and size of the Texas force. They captured a Confederate scouting party at Glorieta Pass, then ran into the main body of Pyron's Confederates near present-day Valencia. After a day-long battle, both sides called a truce to care for their casualties.
Two days later, on March 28, both sides moved toward each other. The Confederates left their supply train at Johnson's Ranch and met the Union forces west of Pigeon's Ranch. Soon both sides were exhausted from hours of battle. As darkness fell, the Confederates learned that their supply wagons had been destroyed at Johnson's Ranch--Union soldiers had set the horses and mules free and burned the wagons. They decided to retreat to Santa Fe. Two weeks later, Sibley ordered a complete retreat to Texas--a difficult march for soldiers facing sickness, the harsh environment, attacks by Union forces, and attacks by Apaches.
By July 1862, all Confederate troops had left New Mexico Territory. The grand Confederate plan to dominate the west ended at Glorieta.