After the assassination of Joseph and Hyrum Smith, non-Mormons feared terrible retaliation by the Nauvoo Legion, and fled the nearby communities of Carthage and Warsaw leaving behind only ghost towns. But Mormons realized that retaliation risked sparking another war of extermination similar to that suffered in Missouri, and thus were at pains to maintain restraint. Despite pressures exerted by western Illinoisians, Governor Ford, on the other hand, resisted calls for a Missouri-style expulsion.

Furthermore, Joseph had left behind a community that was badly fractured. There were pro- and anti-polygamy factions, though the vast majority of Mormons were still unaware of the practice. The anti-polygamy side included Sidney Rigdon, who claimed the right to succeed Joseph as his first counselor. On the pro-polygamy side was Brigham Young, who, as president of the Quorum of the Twelve Apostles, claimed the right to succeed Joseph, despite the fact that it was generally perceived that the Twelve had jurisdiction only over missions. Many believed that Joseph III was intended to rule the church after his father, but the boy was only 12 at the time, and his mother Emma soon distanced herself from Mormonism for a number of years. Emma despised Brigham Young, and was bitterly opposed to any claimants in the hierarchy who supported or had been involved in polygamy. Some wondered if one of the prophet's surviving brothers, either William or Samuel, should succeed the prophet at least as a regent until Joseph III was old enough to become prophet. Samuel died under mysterious circumstances shortly after the assassination of his brother, arousing suspicion that one of the other claimants -- namely Brigham Young -- had had him murdered. Since most Mormons were unaware of the existence of the Council of Fifty or the Quorum of the Anointed, a number of claims advanced by virtue of membership and rank in these bodies -- such as Brigham Young's claim, and the claim of Alpheus Cutler -- were not fully understood by the majority of church members. Some Mormons advanced the claim of David Whitmer, who had been ordained to succeed Joseph in 1834. One of the oddest succession claims was that of James J. Strang who had joined the church only months before the prophet's assassination, and whose charismatic style and claim to have received a number of new revelations seemed to echo the style of the prophet Joseph. He drew a number of prominent Saints into his orbit for at least a while.