As in Kirtland in 1837, by 1844 Joseph's theological, social and political innovations had fractured the Saints into feuding camps and had created boiling dissention. Not long after Joseph's announced bid for the presidency of the United States, William Law, Smith's former second counselor and member of the Council of Fifty, defected over the issue of polygamy and over Joseph's anointing as "king on earth." Law soon threatened to publish a complete account of all the secret political and theological developments in Mormonism in a dissident newspaper he founded called the Nauvoo Expositor, in detail compelling enough to publicly incriminate the prophet and many high-ranking members of the Mormon hierarchy.
Joseph panicked, and had the Nauvoo Legion destroy Law's printing press and all copies of the Expositor. Law and his family fled Nauvoo, in fear for their lives. When word of what had happened spread in surrounding non-Mormon communities, there was a public outcry. The prophet was charged in nearby Carthage with instigating a riot and violation of the first amendment. When attempts to arrest Smith were thwarted, militias were raised in nearby Carthage and Warsaw. In response, Smith called out the Nauvoo Legion, and for a time it seemed Illinois was on the brink of civil war.
At this point Governor Thomas Ford intervened, attempting to persuade Joseph that he must surrender himself if a bloodbath was to be avoided, and promising to keep him safe and ensure a fair trial. Joseph decided instead to flee Nauvoo and go into hiding once again. He crossed the Mississippi and made plans to flee west. During this time, it appears Smith privately renounced many of the secret practices and made some effort to destroy evidence of them by burning the original copy of the polygamy revelation, giving orders to destroy temple garments, and ordering the secretary of the Council of Fifty to burn their minutes.
Smith's flight from the city, however, caused a panic. Hundreds of Saints began to abandon the city. Nauvoo seemed on the verge of descending into chaos as Kirtland had in the wake of the anti-banking scandal. Fearing that the city would soon be defenseless against the mobs, family and friends entreated Joseph to trust the assurances of the governor and to turn himself in, which he finally did on June 24.
On the night of June 27, while Joseph, his brother Hyrum, and church leaders Willard Richards and John Taylor were being held in Carthage, a mob composed of members of the Warsaw militia descended on the jail, and, in conspiracy with the Carthage militia supposedly protecting the prophet, assassinated Joseph and Hyrum.