Almost the only time that the pledge was broken was in the autumn of 1854. Continual trains of immigrants passing through the Sioux country made it nearly impossible to prevent friction between the races in which the blame was quite likely to fall upon the timorous homeseekers. On August 17, 1854, a cow strayed away from a band of Mormons encamped a few miles from Fort Laramie. Some have it that the cow was lame, and therefore abandoned; but whatever the cause, the cow was found, killed, and eaten by a small band of hungry Miniconjou Sioux. The charge of theft was brought into camp at Laramie, not by the Mormons, but by The Bear, chief of the Brulé, and Lieutenant Grattan with an escort of twenty-nine men, a twelve-pounder and a mountain howitzer, was sent out the next day to arrest the Indian who had slaughtered the animal. At the Indian village the culprit was not forthcoming, Grattan's drunken interpreter roughened a diplomacy which at best was none too tactful, and at last the troops fired into the lodge which was said to contain the offender. No one of the troops got away from the enraged Sioux, who, after their anger had led them to retaliate, followed it up by plundering the near-by post of the fur company. Commissioner Manypenny believed that this action by the troops was illegal and unnecessary from the start, since the Mormons could legally have been reimbursed from the Indian funds by the agent.

No general war followed this outbreak. A few braves went on the war-path and rumors of great things reached the East, but General Harney, sent out with three regiments to end the Sioux war in 1855, found little opposition and fought only one important battle. On the Little Blue Water, in September, 1855, he fell upon Little Thunder's band of Brulé Sioux and killed or wounded nearly a hundred of them. There is some doubt whether this band had anything to do with the Grattan episode, or whether it was even at war, but the defeat was, as Agent Twiss described it, "a thunderclap to them." For the first time they learned the mighty power of the United States, and General Harney made good use of this object lesson in the peace council which he held with them in March, 1856. The treaty here agreed upon was never legalized, and remained only a sort of modus vivendi for the following years. The Sioux tribes were so loosely organized that the authority of the chiefs had little weight; young braves did as they pleased regardless of engagements supposed to bind the tribes. But the lesson of the defeat lasted long in the memory of the plains tribes, so that they gave little trouble until the wars of 1864 broke out. Meanwhile Chouteau's old Fort Pierre on the Missouri was bought by the United States and made a military post for the control of these upper tribes.

Before the plains Sioux broke out again, the Minnesota uprising had led the Mississippi Sioux to their defeat. Some were executed in the fall of 1862, others were transported to the Missouri Valley; still others got away to the Northwest, there to continue a profitless war that kept up fighting for several years. Meanwhile came the plains war of 1864 in which the tribes south of the Platte were chiefly concerned, and in which men at the centre of the line thought there were evidences of an alliance between northern and southern tribes. Thus Governor Evans wrote of "information furnished me, through various sources, of an alliance of the Cheyenne and a part of the Arapahoe tribes with the Comanche, Kiowa, and Apache Indians of the south, and the great family of the Sioux Indians of the north upon the plains," and the Indian Commissioner accepted the notion. But, like the question of intrigue, this was a matter of belief rather than of proof; while local causes to account for the disorder are easily found. Yet it is true that during 1864 and 1865 the northern Sioux became uneasy.

During 1865, though the causes likely to lead to hostilities were in no wise changed, efforts were made to reach agreements with the plains tribes. The Cheyenne, humbled at Sand Creek, were readily handled at the Little Arkansas treaty in October. They there surrendered to the United States all their reserve in Colorado and accepted a new one, which they never actually received, south of the Arkansas, and bound themselves not to camp within ten miles of the route to Santa Fé. On the other side, "to heal the wounds caused by the Chivington affair," special appropriations were made by the United States to the widows and orphans of those who had been killed. The Apache, Kiowa, and Comanche joined in similar treaties. During the same week, in 1865, a special commission made treaties of peace with nine of the Sioux tribes, including the remnants of the Mississippi bands. "These treaties were made," commented the Commissioner, "and the Indians, in spite of the great suffering from cold and want of food endured during the very severe winter of 1865–66, and consequent temptation to plunder to procure the absolute necessaries of life, faithfully kept the peace."

In September, 1865, the steamer Calypso struggled up the shallow Missouri River, carrying a party of commissioners to Fort Sully, there to make these treaties with the Sioux. Congress had provided $20,000 for a special negotiation before adjourning in March, 1865, and General Sully, who was yet conducting the prolonged Sioux War, had pointed out the place most suitable for the conference. The first council was held on October 6.

The military authorities were far from eager to hold this council. Already the breach between the military power responsible for policing the plains and the civilian department which managed the tribes was wide. Thus General Pope, commanding the Department of the Missouri, grumbled to Grant in June that whenever Indian hostilities occurred, the Indian Department, which was really responsible, blamed the soldiers for causing them. He complained of the divided jurisdiction and of the policy of buying treaties from the tribes by presents made at the councils. In reference to this special treaty he had "only to say that the Sioux Indians have been attacking everybody in their region of country; and only lately ... attacked in heavy force Fort Rice, on the upper Missouri, well fortified and garrisoned by four companies of infantry with artillery. If these things show any desire for peace, I confess I am not able to perceive it."

In future years this breach was to become wider yet. At Sand Creek the military authorities had justified the attack against the criticism of the local Indian agents and Eastern philanthropists. There was indeed plenty of evidence of misconduct on both sides. If the troops were guilty on the charge of being over-ready to fight—and here the words of Governor Evans were prophetic, "Now the war ... is nearly through, and the Great Father will not know what to do with all his soldiers, except to send them after the Indians on the plains,"—the Indian agents often succumbed to the opportunity for petty thieving. The case of one of the agents of the Yankton Sioux illustrates this. It was his custom each year to have the chiefs of his tribe sign general receipts for everything sent to the agency. Thus at the end of the year he could turn in Indians' vouchers and report nothing on hand. But the receipt did not mean that the Indian had got the goods; although signed for, these were left in the hands of the agent to be given out as needed. The inference is strong that many of the supplies intended for and signed for by the Indians went into the pocket of the agent. During the third quarter of 1863 this agent claimed to have issued to his charges: "One pair of bay horses, 7 years old; ... 1 dozen 17-inch mill files; ... 6 dozen Seidlitz powders; 6 pounds compound syrup of squills; 6 dozen Ayer's pills; ... 3 bottles of rose water; ... 1 pound of wax; ... 1 ream of vouchers; ... ½ M 6434 8½-inch official envelopes; ... 4 bottles 8-ounce mucilage." So great was this particular agent's power that it was nearly impossible to get evidence against him. "If I do, he will fix it so I'll never get anything in the world and he will drive me out of the country," was typical of the attitude of his neighbors.

With jurisdiction divided, and with claimants for it quarrelling, it is no wonder that the charges suffered. But the ill results came more from the impossible situation than from abuse on either side. It needs often to be reiterated that the heart of the Indian question was in the infiltration of greedy, timorous, enterprising, land-hungry whites who could not be restrained by any process known to American government. In the conflict between two civilizations, the lower must succumb. Neither the War Department nor the Indian Office was responsible for most of the troubles; yet of the two, the former, through readiness to fight and to hold the savage to a standard of warfare which he could not understand, was the greater offender. It was not so great an offender, however, as the selfish interests of those engaged in trading with the Indians would make it out to be.

The Fort Sully conference, terminating in a treaty signed on October 10, 1865, was distinctly unsatisfactory. Many of the western Sioux did not come at all. Even the eastern were only partially represented. And among tribes in which the central authority of the chiefs was weak, full representation was necessary to secure a binding peace. The commissioners, after most pacific efforts, were "unable to ascertain the existence of any really amicable feeling among these people towards the government." The chiefs were sullen and complaining, and the treaty which resulted did little more than repeat the terms of the treaty of 1851, binding the Indians to permit roads to be opened through their country and to keep away from the trails.

It is difficult to show that the northern Sioux were bound by the treaty of Fort Sully. The Laramie treaty of 1851 had never had full force of law because the Senate had added amendments to it, which all the signatory Indians had not accepted. Although Congress had appropriated the annuities specified in the treaty the binding force of the document was not great on savages. The Fort Sully treaty was deficient in that it did not represent all of the interested tribes. In making Indian treaties at all, the United States acted upon a convenient fiction that the Indians had authorities with power to bind; whereas the leaders had little control over their followers and after nearly every treaty there were many bands that could claim to have been left out altogether. Yet such as they were, the treaties existed, and the United States proceeded in 1865 and 1866 to use its specified rights in opening roads through the hunting-grounds of the Sioux.