While the Missouri militia continued to expel Mormons from the state, the prophet and his companions were charged with treason, murder, arson, and other sundry crimes. Joseph narrowly escaped summary execution at the order of General Clark, the commander of the Missouri militia, due to the insubordination of General Alexander W. Doniphan. Clark wanted to treat Joseph as a prisoner of war and try him in a court martial, but Joseph's lawyers were eventually able to make the case for a civil trial. Evidence introduced at preliminary hearings before Judge King included testimony regarding the Mormons' theocratic interpretations of scripture and the activities of the Danites, including subpoenaed testimony from former Danite leader Sampson Avard. While awaiting trial, Joseph and Hyrum Smith and Sidney Rigdon were held for six months in Liberty jail under extreme and inhumane conditions. They were brought to Daviess County for trial, but Joseph's lawyers successfully pleaded for a change of venue to Boone County.

Meanwhile, the trial was becoming an embarassment to the state, as word continued to spread about the Missourians' treatment of the Saints. Having rid himself of the Mormons, it appears Governor Boggs was anxious for an excuse to drop the matter and quell any further public revelations about the extermination action. While on route to his new trial venue, Joseph and his companions were allowed to escape their captors and rejoin the Saints in Quincy. Though Joseph was free, he was now technically a fugitive from the law in two states (Ohio and Missouri).

In April a number of the twelve apostles, among whom was Brigham Young, surreptitiously returned to Far West to lay the cornerstones of a temple in symbolic fulfillment of Joseph's prophesy the preceding year.

While in prison, Joseph made arrangements for the Saints to purchase large tracts of land in and around Commerce, Illinois. The Saints moved to Commerce (which they renamed "Nauvoo," "the Beautiful") and also settled in Montrose, just across the Mississippi River in the Iowa Territory.

The Saints continued to seek redress from the state of Missouri. They gathered hundreds of affidavits from individuals who had been injured by the expulsion. Joseph Smith and Sidney Rigdon travelled to Washington, D.C. where they petitioned President Martin VanBuren and Congress. Joseph argued that the Saints' consitutional rights had been violated by the state of Missouri, but was informed that the problems of the Saints hinged on matters of states' rights and that the Federal government could not intervene.