In 1843, Joseph was arrested again, this time in relation to the old Missouri treason charge. After a dramatic series of events in which Joseph was kidnapped by the sheriffs, who were in turn apprehended by a contingent of the Nauvoo Legion and charged with unlawful arrest, Joseph and his captors were brought back to Nauvoo, where the Municipal Court again invalidated the writ of arrest against Joseph. Once again, the Nauvoo city council passed a questionable ordinance, this time which would subject to life imprisonment any officer guilty of bringing a writ for the arrest of Joseph Smith based on the Missouri charges, and which would allow for release only by pardon of the mayor (who at that time happened to be Joseph Smith).

The non-Mormon populace was outraged at what they perceived to be the perpetual thwarting of civil justice by a theocratically controlled court, this time backed by a Mormon militia. There was a growing determination to hold Joseph Smith and Nauvoo accountable. One result was the introduction of legislation to repeal the Nauvoo charters, which were widely perceived as illegal and abusive, and which had been a political issue in the election of Governor Thomas Ford.

Joseph countered by petitioning the U.S. Congress to grant Nauvoo territorial status. He also hastened his plans for a westward migration, sending emissaries to Washington D.C., Texas, and Europe in search of diplomatic support for the establishment of a Mormon empire in the west.

Joseph managed to win his brother Hyrum's support for polygamy, after promising to initiate Hyrum into polygamous marriages of his own. Hyrum persuaded Joseph to write the revelation on polygamy down, believing that Joseph could win acceptance for the practice if he presented it openly. When Hyrum presented the revelation to the Church High Council, however, it immediately created an open rift among the leadership. Most of the advocates of polygamy in the church leadership were individuals who had already secretly been initiated into the practice by Joseph.