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."

The population of the silver camp had begun to urge Congress to provide a territory independent of New Mexico, immediately after the development of the Mowry mines. Delegates and petitions had been sent to Washington in the usual style. But congressional indifference to new territories had blocked progress. The new discoveries reopened the case in 1862 and 1863. Forgetful of his Indian wards and their rights, the Superintendent of Indian Affairs had told of the sad peril of the "unprotected miners" who had invaded Indian territory of clear title. They would offer to the "numerous and warlike tribes" an irresistible opportunity. The territorial act was finally passed on February 24, 1863, while the new capital was fixed in the heart of the new gold field, at Fort Whipple, near which the city of Prescott soon appeared.

The Indian danger in Arizona was not ended by the erection of a territorial government. There never came in a population large enough to intimidate the tribes, while bad management from the start provoked needless wars. Most serious were the Apache troubles which began in 1861 and ceased only after Crook's campaigns in the early seventies. In this struggle occurred the massacre at Camp Grant in 1871, when citizens of Tucson, with careful premeditation, murdered in cold blood more than eighty Apache, men, women, and children. The degree of provocation is uncertain, but the disposition of Tucson, as Mowry has phrased it, was not such as to strengthen belief in the justice of the attack: "There is only one way to wage war against the Apache. A steady, persistent campaign must be made, following them to their haunts—hunting them to the 'fastnesses of the mountains.' They must be surrounded, starved into coming in, surprised or inveigled—by white flags, or any other method, human or divine—and then put to death. If these ideas shock any weak-minded individual who thinks himself a philanthropist, I can only say that I pity without respecting his mistaken sympathy. A man might as well have sympathy for a rattlesnake or a tiger."

The mines of Arizona, though handicapped by climate and inaccessibility, brought life into the extreme Southwest. Those of Nevada worked the partition of Utah. Farther to the north the old Oregon country gave out its gold in these same years as miners opened up the valleys of the Snake and the head waters of the Missouri River. Right on the crest of the continental divide appeared the northern group of mining camps.

The territory of Washington had been cut away from Oregon at its own request and with Oregon's consent in 1853. It had no great population and was the subject of no agricultural boom as Oregon had been, but the small settlements on Puget Sound and around Olympia were too far from the Willamette country for convenient government. When Oregon was admitted in 1859, Washington was made to include all the Oregon country outside the state, embracing the present Washington and Idaho, portions of Montana and Wyoming, and extending to the continental divide. Through it ran the overland trail from Fort Hall almost to Walla Walla. Because of its urging Congress built a new wagon road that was passable by 1860 from Fort Benton, on the upper Missouri, to the junction of the Columbia and Snake. Farther east the active business of the American Fur Company had by 1859 established steamboat communication from St. Louis to Fort Benton, so that an overland route to rival the old Platte trail was now available.

In eastern Washington the most important of the Indians were the Nez Percés, whose peaceful habits and friendly disposition had been noted since the days of Lewis and Clark, and who had permitted their valley of the Snake to become a main route to Oregon. Treaties with these had been made in 1855 by Governor Stevens, in accordance with which most of the tribe were in 1860 living on their reserve at the junction of the Clearwater and Snake, and were fairly prosperous. Here as elsewhere was the specific agreement that no whites save government employees should be allowed in the Indian Country; but in the summer of 1861 the news that gold had been found along the Clearwater brought the agreement to naught. Gold had actually been discovered the summer before. In the spring of 1861 pack trains from Walla Walla brought a horde of miners east over the range, while steamboats soon found their way up the Snake. In the fork between the Clearwater and Snake was a good landing where, in the autumn of 1861, sprang up the new Lewiston, named in honor of the great explorer, acting as centre of life for five thousand miners in the district, and showing by its very existence on the Indian reserve the futility of treaty restrictions in the face of the gold fever. The troubles of the Indian department were great. "To attempt to restrain miners would be, to my mind, like attempting to restrain the whirlwind," reported Superintendent Kendall. "The history of California, Australia, Frazer river, and even of the country of which I am now writing, furnishes abundant evidence of the attractive power of even only reported gold discoveries.

"The mines on Salmon river have become a fixed fact, and are equalled in richness by few recorded discoveries. Seeing the utter impossibility of preventing miners from going to the mines, I have refrained from taking any steps which, by certain want of success, would tend to weaken the force of the law. At the same time I as carefully avoided giving any consent to unauthorized statements, and verbally instructed the agent in charge that, while he might not be able to enforce the laws for want of means, he must give no consent to any attempt to lay out a town at the juncture of the Snake and Clearwater rivers, as he had expressed a desire of doing."

Continued developments proved that Lewiston was in the centre of a region of unusual mineral wealth. The Clearwater finds were followed closely by discoveries on the Salmon River, another tributary of the Snake, a little farther south. The Boisé mines came on the heels of this boom, being followed by a rush to the Owyhee district, south of the great bend of the Snake. Into these various camps poured the usual flood of miners from the whole West. Before 1862 was over eastern Washington had outgrown the bounds of the territorial government on Puget Sound. Like the Pike's Peak diggings, and the placers of the Colorado Valley, and the Carson and Virginia City camps, these called for and received a new territorial establishment.