On August 6, 1838, election day, violence broke out at the polls in DeWitt, Missouri, as non-Mormons tried to stop Mormons from voting and some Danites who were present brutally retaliated. Armed mobs of Missourians attacked Mormon settlements, and the Mormons retaliated in kind, rapidly escalating the situation into an all-out civil war.

The governor, Lilburn Boggs, was a former resident of Jackson County and a supporter of the mob action that had driven the Saints out of Independence. When reports of Danite and Mormon predations reached Boggs, he declared the Mormons a public nuisance and issued his now infamous "extermination order," sending in the state militia to implement it. It was during this time that the notorious Haun's Mill Massacre took place, in which Missourians indiscriminately shot at and killed unarmed Mormon men, women and children. Badly outnumbered and outgunned, Mormons who had not been able to flee in time were subjected to a reign of terror by mobs and by a hostile military force. Joseph Smith, Sidney Rigdon, and other church leaders turned themselves in to the authorities on condition that the Saints be allowed to leave the state unmolested. While Joseph and his companions were taken into custody, some 5,000 Mormon refugees fled to Quincy, Illinois.