The outbreak of the Civil War extinguished for the time the Mowry mines and others in the Santa Cruz Valley, holding them in check till a second mineral area in western New Mexico should be found. United States army posts were abandoned, confederate agents moved in, and Indians became bold. The federal authority was not reëstablished until Colonel J. H. Carleton led his California column across the Colorado and through New Mexico to Tucson early in 1862. During the next two years he maintained his headquarters at Santa Fé, carried on punitive campaigns against the Navaho and the Apache, and encouraged mining.
The Indian campaigns of Carleton and his aides in New Mexico have aroused much controversy. There were no treaty rights by which the United States had privileges of colonization and development. It was forcible entry and retention, maintained in the face of bitter opposition. Carleton, with Kit Carson's assistance, waged a war of scarcely concealed extermination. They understood, he reported to Washington, "the direct application of force as a law. If its application be removed, that moment they become lawless. This has been tried over and over and over again, and at great expense. The purpose now is never to relax the application of force with a people that can no more be trusted than you can trust the wolves that run through their mountains; to gather them together little by little, on to a reservation, away from the haunts, and hills, and hiding-places of their country, and then to be kind to them; there teach their children how to read and write, teach them the arts of peace; teach them the truths of Christianity. Soon they will acquire new habits, new ideas, new modes of life; the old Indians will die off, and carry with them all the latent longings for murdering and robbing; the young ones will take their places without these longings; and thus, little by little, they will become a happy and contented people."
Mowry's mines had been seized by Carleton at the start, as tainted with treason. The whole Tucson district was believed to be so thoroughly in sympathy with the confederacy that the commanding officer was much relieved when rumors came of a new placer gold field along the left bank of the Colorado River, around Bill Williams Creek. Thither the population of the territory moved as fast as it could. Teamsters and other army employees deserted freely. Carleton deliberately encouraged surveying and prospecting, and wrote personally to General Halleck and Postmaster-general Blair, congratulating them because his California column had found the gold with which to suppress the confederacy. "One of the richest gold countries in the world," he described it to be, destined to be the centre of a new territorial life, and to throw into the shade "the insignificant village of Tucson."