Encyclopedia of Mormonism, Vol.2, MISSOURI CONFLICT
Hostilities escalated into outright warfare. Far West Militia Captain David W. Patten, an apostle, pursued a renegade band of Missouri militia overnight to the Crooked River in northern Ray County where, at dawn on October 25, they clashed. Two died on the battlefield, one on each side, and two mortally wounded Saints died soon after, including Patten.
From the Battle of Crooked River, rumors of LDS aggression spread like wildfire. On the strength of these rumors, Governor Boggs issued his infamous Extermination Order on October 27, authorizing the state militia to drive all Mormons from Missouri or exterminate them. Three days later Colonel William O. Jennings launched an unprovoked attacked on an LDS settlement at Haun's Mill, east of Far West, leaving seventeen men and boys dead (see Haun's Mill Massacre). Survivors joined other refugees fleeing to Far West. On October 31, the militia under the command of Major General Samuel D. Lucas laid siege upon Far West.
To avoid bloodshed, Joseph Smith and others agreed to meet with militia leaders, who instead arrested them. A court-martial that evening summarily sentenced Joseph Smith and his associates to be shot, and Lucas ordered Brig. General Alexander Doniphan to execute them at dawn. Doniphan thought the order illegal and heroically refused to carry it out, declaring that he would bring to account anyone who tried to do it. After Far West defenders were disarmed, Missouri attackers committed numerous outrages against women and property; a number of men were shot and at least one was killed.
While Joseph Smith and some of the others were jailed at Independence, in richmond jail, and finally in Liberty Jail, the rest of the Latter-day Saints were forced from the state. That winter, under the leadership of Brigham Young, approximately 12,000 suffering Saints fled Missouri, most crossing the Mississippi River into Illinois at Quincy.
Joseph Smith and several others spent five months in jail awaiting trial for alleged murder, treason, arson, and other charges growing out of the fall violence and attempts at defense. For the Prophet, this imprisonment evoked a legacy of strength and revelations from heaven (see Doctrine and Covenants: Sections 121-23). A trial was never held. On April 15, 1839, while being transported on a change of venue to Boone County, Joseph and his brother Hyrum were allowed to escape to join Saints and their families in Illinois.