In 1849, the Mormons proposed that a large part of the territory which they inhabited be incorporated into the United States as the State of Deseret. Their primary concern was to be governed by men of their own choosing rather than "unsympathetic carpetbag appointees" whom they believed would be sent from Washington, D.C. if their region were given territorial status, as was customary. They believed that only through a state run by church leadership could they maintain their religious freedom. The U.S. Congress created the Utah Territory as part of the Compromise of 1850. President Millard Fillmore selected Brigham Young, President of the LDS Church, as the first governor of the Territory. The Mormons were pleased by the appointment, but gradually the amicable relationship between Mormons and the federal government broke down.
During the Presidential Election of 1856 a key plank of the newly formed Republican Party's platform was a pledge "to prohibit in the territories those twin relics of barbarism: polygamy and slavery." The Republicans linked the Democratic principle of popular sovereignty to the acceptance of polygamy in Utah, and turned this accusation into a formidable political weapon. Popular sovereignty was the theoretical basis of the Compromise of 1850 and the Kansas-Nebraska Act of 1854. This concept was meant to remove the divisive issue of slavery in the Territories from national debate, forestalling armed conflict between the North and South. But during the campaign, the Republican Party denounced the theory as protecting polygamy. Leading Democrats such as Stephen A. Douglas, formerly an ally of the Latter-day Saints, began to denounce Mormonism to save the concept of popular sovereignty. The Democrats believed that American attitudes toward polygamy had the potential of derailing the compromise on slavery. For the Democrats, attacks on Mormonism therefore had the dual purpose of disentangling polygamy from popular sovereignty, and distracting the nation from the ongoing battles over slavery.
In addition to popular election, many early LDS Church leaders received quasi-political administrative appointments at both the territorial and federal level, that coincided with their ecclesiastical roles; in particular were the powerful probate judges. As the U.S. Constitution outlines, these executive and judicial appointments were confirmed by the Territorial Legislature, which largely consisted of popularly elected Latter-day Saints. Additionally, LDS Church leaders counseled Latter-day Saints to use ecclesiastical arbitration to resolve disputes amongst church members before resorting to the more explicit legal system. Both Pres. Buchanan and the U.S. Congress saw these acts as obstructing, if not subverting, the operation of legitimate institutions of the United States.
These circumstances were not helped by the relationship between "Gentile"(non-Mormon) federal appointees and the Mormon territorial leadership. The territory's Organic Act held that the governor, federal judges, and other important territorial positions were to be filled by appointees chosen by the President with the advice and consent of the Senate, but without any reference to the will of Utah's population—as was standard for all territorial administration. Some federal officials sent by the President maintained essentially harmonious relationships with the Latter-day Saints. For instance, from 1853–1855, the territorial supreme court was composed of two non-Mormons and one Mormon. However, both of these non-Mormons were well respected in the Latter-day Saint community, and were genuinely mourned upon their deaths. Others had severe difficulties adjusting to the Mormon-dominated territorial government and the unique Mormon culture. Historian Norman Furniss relates that although some of these appointees were basically honest and well-meaning, many were highly prejudiced against the Mormons even before they arrived in the territory, were woefully unqualified for their positions, and some were down-right reprobate.
Beginning in 1851, a number of federal officers, some claiming that they feared for their physical safety, left their Utah appointments for the east. The stories of these "Runaway Officials" convinced the new President that the Mormons were nearing a state of rebellion against the authority of the United States. According to LDS historians James B. Allen and Glen M. Leonard, the most influential information came from William W. Drummond, an associate justice of the Utah territorial supreme court who began serving in 1854. Drummond's letter of resignation of March 30, 1857 contained charges that Young's power set aside the rule of law in the territory, that the Mormons had ignored the laws of Congress and the Constitution, and that male Mormons acknowledged no law but the priesthood. This account was further supported by Territorial Chief Justice Kinney in reports to Washington, where he recited examples of what he believed to be Brigham Young's perversion of Utah's judicial system and further urged his removal from office and the establishment of a U.S. Army garrison in the territory. There were further charges of treason, battery, theft, and fraud made by other officials including Federal Surveyors,[28] and Federal Indian Agents. Furniss states that most federal reports from Utah to Washington "left unclear whether the [Mormons] habitually kicked their dogs; otherwise their calendar of infamy in Utah was complete."
As early as 1852, Dr. John M. Bernhisel, Utah's Mormon delegate to Congress, had suggested that an impartial committee be sent to investigate the actual conditions in the territory. This call for an investigation was renewed during the crisis of 1857 by Bernhisel and even by Senator Stephen A. Douglas. However, the President would not wait. Under massive popular and political pressure, President Buchanan decided to take decisive action against the Mormons soon after his inauguration on March 4, 1857.
President Buchanan first decided to appoint a new governor in place of Brigham Young. The position was offered to several individuals who refused, and the President finally settled on Alfred Cumming during the summer. While Young became aware of the change in territorial administration through press reports and other sources, he received no official notification of his replacement until Cumming arrived in the Territory in November 1857. Buchanan also decided to send a force of 2,500 army troops to build a post in Utah and to act as a posse comitatus once the new governor had been installed.