The prophet gave thought to the deteriorating relations between the Mormons and the northern Missourians, and then made an announcement. "There is great excitement at present among the Missourians, who are continually chafing us, and provoking us to anger " said Smith, "but we do not fear them, for the Lord God, the Eternal Father is our God, and their father the devil."
The Church wrote an appeal to Governor Boggs for assistance, but a reply was sent back saying, "The quarrel is between the Mormons and the mob," suggesting they "might fight it out." When the Missourians saw that the governor was choosing not to interfere, they were emboldened to send Anti-mormon forces marching toward Daviess County—the more northern of the two Mormon-settled counties—to remove all Mormons from the land.
Church leaders were alarmed by the news of their approach, but Joseph Smith reminded the Saints that Jesus had said that "Greater love hath no man than this, that he lay down his life for his brethren." And he asked for volunteers to march north to protect the city of Adam-ondi-Ahman. About 100 of the Saints joined him.
For the next two days, guerrilla warfare was waged on both sides. Danites raided two towns considered to be centers of anti-Mormon activity. They burned homes and looted goods. These actions were considered justified by Church members because, as one militia officer put it, "We were being hemmed in on all sides by our enemies and were without food."
Two of the Twelve Apostles—Orson Hyde and Thomas Marsh—turned on the Church and aided the enemy in October, swearing out an affidavit that "the Prophet inculcates the notion, and it is believed by every true Mormon, that Smith’s prophecies are superior to the laws of the land. I have heard the Prophet say that he would yet tread down his enemies, and walk over their dead bodies; and if he was not let alone, he would be a second Mohammed to this generation."
The first battle of what became known as The Mormon War occurred on October 25, 1838. The Missourians had raided Mormon homes, intimidated residents, and taken three prisoners. Members of the Mormon militia were sent to free the prisoners, which they did, but in a firefight at dawn, several men were wounded, and two killed—David Patten of the Twelve Apostles, and Church member Gideon Carter, who was shot in the head, and so defaced that he was unrecognizable.
Based on false reports of the battle claiming the Saints had massacred the Missourians, Governor Boggs wrote his infamous "extermination order" in which he declared: "The Mormons must be treated as enemies and must be exterminated or driven from the state, if necessary for the public good. Their outrages are beyond all description." Soon after, more than 2,000 men from various state militias had encircled the city of Far West where Joseph Smith had instructed all the area Saints to gather for safety.
In what was likely an attempt to carry out the governor's orders, on October 30, a Missourian mob attacked the village of Haun's Mill, firing mercilessly at men, women, and children alike. Seven-year-old Alma Smith was shot in the hip and witnessed his father's murder. While the women fled into the woods with their children, the Mormon men sought to defend themselves from the blacksmith shop.
Alma Smith's 10-year-old brother hid under the bellows in the blacksmith shop, but was found by members of the mob, one of whom pressed his gun against the boy's skull and blew the upper part of his head off. The perpetrator was later heard to justify his action with the words: "Nits will make lice, and if he had lived he would have become a Mormon." A total of 17 Saints were killed, and the prophet later remarked, "At Haun’s Mill the brethren went contrary to my counsel; if they had not, their lives would have been spared."
The next day, Anti-Mormon forces preparing to attack Far West outnumbered the Saints five-to-one. George Hinkle, the leader of the Mormon militia, convinced the senior Church leaders—including Joseph Smith and Sidney Rigdon—to come out of the city for peace talks with the leader of the Missourian militias. Smith and the others were then shocked to discover that Hinkle had betrayed them, secretly having made an agreement with the Missourians to hand over the Mormon leadership for trial and for the rest of the Saints to disarm and leave the state.
In the morning, Hinkle surrendered Far West, removing Mormon troops from the city. The Missourian militias then poured inside, vandalizing the city, looting property, and raping some of the women. Three days later, Missourian officials ordered all Mormons to leave the state. They were allowed to stay until the following spring, however, so they would not have to travel during the winter months.
Smith and the other Church leaders were held in jail for two weeks during which they were abused, subject to obscene jokes, dreadful blasphemies, and filthy language. At one point, having had enough, the prophet stood up and shouted, "Silence, ye fiends of the infernal pit. In the name of Jesus Christ I rebuke you, and command you to be still; I will not live another minute and bear such language. Cease such talk, or you or I die this instant!" The guards apologized and remained silent thereafter.
After appearing before a judge, Joseph Smith, Sidney Rigdon, the prophet's brother Hyrum, and three other Church leaders were transferred to another jail in Liberty, Missouri, to await trial on charges of treason. This squalid, dark, dungeon-like 22-square-foot basement jail cell would be their home for the next four months as they suffered from cold and were given only filthy food that they could not bring themselves to eat until driven to it by hunger.
From mid-February through spring of 1839, the Missouri Saints were forced to leave their homes and businesses behind once again as they packed up to leave the state. At this time, word came to Church leaders that the people of Illinois were sympathetic to the plight of the Mormons. Some also hoped that a large influx of new Mormon settlers would help the struggling state economy. Under Brigham Young's leadership, about 9,000 Saints migrated to western Illinois.