A few disaffected Mormons in Nauvoo joined together to publish a newspaper, the Nauvoo Expositor. Its first and only issue was published 7 June 1844. The paper was highly antagonistic toward Smith; the bulk of the Expositor's single issue was devoted to criticism of Smith's practice of polygamy and his political power. The city council, headed by Smith who was mayor of Nauvoo responded by passing an ordinance declaring the newspaper a public nuisance designed to promote violence against Smith and his followers. Under the council's new ordinance, Smith and the city council ordered the city marshal to destroy the paper and the press.

This action was seen by many non-Mormons as illegal; Smith was accused of violating the freedom of the press. Violent threats were made against Smith and the Mormon community in Nauvoo. Charges were brought against Smith and he submitted to incarceration in Carthage, the Hancock County seat. Smith's brother, Hyrum, and eight of his associates including John Taylor and Willard Richards, accompanied him to the jail. The Governor of the state, Thomas Ford had promised protection and a fair trial. All of Smith's associates left the jail, except his brother Hyrum, Richards and Taylor.

On June 27, 1844, an armed group of about 200 men stormed the jail, and went to Smith's cell. Despite a brief struggle, the group was able to open fire on Smith and his associates. Hyrum Smith was shot in the face, and died immediately. As the mob burst through the doorway, Joseph Smith (who had earlier been given a six-shooter by a visitor) managed to fire three shots at the mob. Richards was unharmed, while Taylor was shot several times, but survived. (One of the bullets may have glanced off the pocket watch in his left breast pocket.) Smith, however, was shot multiple times while trying to jump out an open window. After he fell from the window, he was shot several more times, killing him.

Smith and his brother were initially buried below the Smith Homestead in Nauvoo. They were later disinterred on the orders of Smith's grandson Frederick M. Smith and reburied along with Smiths' wife Emma in a location thought to be safer from Mississippi flooding.

Immediate reaction

Smith's death created a crisis for the Latter Day Saints. Their charismatic founder was dead and their hierarchy was scattered on missionary efforts and in support of Smith's presidential campaign. Brigham Young recorded in his journal his initial concern after Smith's murder: "The first thing which I thought of was, whether Joseph had taken the keys of the kingdom with him from the earth." Without the keys of the kingdom, that is, the appropriate Priesthood authority, Young recognized the possibility that, according to the church's doctrine and Smith's own teachings, the church lacked a divinely-sanctioned leader.

Because of ongoing tensions, the state legislature revoked Nauvoo's city charter and it was disincorporated. All protection, public services, self-government and other public benefits were revoked. Those who lived in the former City of Nauvoo referred to it as the City of Josephhe being its founderafter this time, until the city was again granted a charter. Without official defenses, city residents continued to be persecuted by opponents, leading Young to consider other areas for settlement, including Texas, California, Iowa, and the Great Basin region.