In the immediate aftermath of the massacre at Ash Hollow, Harney and his men looted the village for portable items of value; the Native American homes and property that remained were destroyed in a bonfire, while Harney ordered that the people his soldiers killed should be left unburied so that wolves could eat their remains. Harney then ordered his soldiers to march across the Midwest, charting the land for future settlers, hunting for treasure and fossils, and intimidating resident Native Americans.
As Harney’s forces moved through the Midwest, he was approached by the survivors of Ash Hollow and other Native Americans who wished to establish peaceful relations with his forces, but he refused to negotiate immediately, inviting them to a massive treaty council next spring. Informed that his intended winter quarters at Fort Pierre were inadequately provisioned, Harney continued his 2000 mile march through the Sioux homelands, because he felt if he did not intimidate local tribes he would, "lose much of my prestige....the results would more than compensate for any loss of animals and the temporary exposure of my men." The lack of adequate food and shelter caused deaths from malnutrition related illnesses and frostbite amputations amongst Harney's forces that winter. Many soldiers also had unresolved trauma from the massacre of women and children at Ash Hollow, which remained a topic of discussion throughout the winter. Consequently, his soldiers sang a song that included the line: “We will never forgive old Harney for bringing us to Fort Pierre.”
On March 1, 1856, Sioux leadership assembled at Fort Pierre to attend a grand council with Harney. Harney immediately threatened the attendees who he told that if they accepted the terms he dictated "they will find me the best friend they ever had; but if they don't do it, they will find me the worst enemy they ever had."
On the second day, Harney theatrically displayed the "great power of the white man" that included the ability to "kill and bring to life again." Harney had his surgeon put a dog into anesthesia with chloroform and demonstrated the dog's apparent death to the attendees. When the surgeon failed to revive the dog, Harney's hubris was met with derisive laughter by the assembled Native American leaders. After signing treaties that guaranteed free access to indigenous territories to settlers headed to the far west, Harney sent messengers to the Pawnee, Cheyenne, and Arapaho tribes threatening to "sweep them from the face of the Earth" if they did not sign similar treaties protecting encroaching settlers.
In the next few years, Harney was assigned to hot spots where his commanders believed his attributes and reputation were valuable. In 1856 and 1857, he ordered his troops to systematically destroy the homes of Seminole people after carefully combing the Everglades for any signs of human habitation. In the spring of 1857, he was reassigned to Kansas, where the conflict between pro-slavery and anti-slavery forces had caused significant bloodshed, property destruction, and civil unrest. Harney’s forces successfully kept law and order, allowing Kansans to vote on a state constitution without significant disruptions.
In the summer of 1857, Harney was ordered to march a large column of men to Utah Territory, where he was supposed to personally intimidate Brigham Young and the Mormon leadership, whose polygamy and communal lifestyle had scandalized the US government. At a party in Kansas, Harney bragged that he would “hang Brigham [Young] first and try him afterward."
Simultaneously, the United States waged war against the Cheyenne people, destroying their homes and possessions. In retaliation, part of Harney's supply train, which went to Utah ahead of his forces, was destroyed. Harney blamed the commanders of that war, claiming that if the Cheyenne had "fear[ed] for their family" (in other words if US commanders had killed Cheyenne women and children as Harney had at Ash Hollow) than the supply train would not have been attacked. This unrest caused Harney to be reassigned to the Midwest where his presence intimidated Native Americans instead of Utah.
In 1858, Harney was assigned to the Pacific Northwest where his instructions were to “thoroughly chastise” the local Native Americans, with explicit instructions to harass civilians, destroy Native American livestock and to “not make any overtures of friendship” until Pacific Northwest tribes were punished for resisting white settler encroachment. By the time Harney arrived, however, peace had already been established; in lieu of combat, Harney decided to summarily hang some Yakamas captured during the war and extend the zone of white settlement east of the Cascades, an area previously reserved for indigenous residents.
On July 16, 1859, Harney ordered American troops to occupy San Juan Island, which was legally speaking, legitimately claimed by American and British settlers. Harney’s orders came after American settler Lyman Cutlar killed a pig belonging to the British Hudson’s Bay Company. Company operatives and British government officials (who were often the same people) tried to intimidate Cutlar, whose farm interfered with their long-established sheep farming operations.
Harney’s actions caused the British to reciprocate, and that summer American soldiers on the island and British forces in the water faced off against each other, intimidating each other without firing a shot. Harney, who viewed San Juan Island as “the most commanding position we possess on the sound," was likely motivated to invade for strategic reasons. He also believed in America’s manifest destiny, which in Harney’s eyes at the time meant that "the knell of power was sounded in Europe when the first pilgrim vessel sought a harbor on the western shores of the Atlantic."
As American and British forces came near to conflict thanks to his actions, Harney did nothing to cool down the situation. Instead, it took the intervention of the highest ranking general of the US military, Winfield Scott, who at the instigation of US President James Buchannan, who disapproved strongly of Harney’s actions, traveled from his headquarters in New York City to the Pacific Northwest, where, after chastising Harney and reassigning him to St. Louis, successfully negotiated a peaceful joint occupation of San Juan Island that lasted until 1872.