Starting in 1831,
Jackson County, Missouri, had become home to several members of the
Church of Jesus Christ of Latter Day Saints, a religious organization founded by
Joseph Smith in upstate New York a year earlier. By 1833, approximately 1200 Mormons lived in Jackson County, where they aroused the ire of many earlier settlers by their belief that
American Indians, whom they called "
Lamanites", were the descendants of ancient Israelites who had migrated to the New World centuries earlier (see
Book of Mormon). Other fundamental differences between Mormons and non-Mormons exacerbated the situation, especially a belief that the Mormons were
abolitionists, who planned to foment uprisings among Missouri slaves. Denunciations of abolitionism in the church press did nothing to allay their neighbors' fears, and matters came to a head in late 1833, when the Mormons were forcibly expelled from the county. Following these events, Joseph Smith and other church leaders petitioned the
governor of Missouri for protection, but were largely ignored. This led them to hire Doniphan and Atchison, among others, to defend their rights in court. Doniphan assisted in the creation of a special
county in northwestern Missouri for the Mormons, but continued friction between Mormons and non-Mormon settlers in that region ultimately led to the outbreak of the
1838 Mormon War. Following a clash between Mormons and state militia at the
Battle of Crooked River, governor
Lilburn Boggs issued his infamous "
Extermination Order", directing that the Mormons be "exterminated, or driven from the state". As a
brigadier general in the Missouri Militia, Doniphan was ordered into the field with other forces to operate against the Mormons, even though he had worked diligently to avoid the conflict, and believed that the Mormons were largely acting in self-defense. After the surrender of
Far West, General Samuel Lucas took custody of Joseph Smith and other Mormon leaders, and instituted a
drumhead court martial (
kangaroo court), which declared Smith and the others guilty of
treason, and ordered Doniphan to execute them. Doniphan indignantly refused, saying: "It is cold blooded murder. I will not obey your order. ... [I]f you execute these men, I will hold you responsible before an earthly tribunal, so help me God". The Mormon leaders were accordingly sent to Liberty Jail during the winter, to await trial during the following spring of 1839, at which trial Doniphan was appointed as their defense attorney and energetically defended them at the risk of his good reputation and, in all probability, his life. Ultimately, the church leaders were permitted to escape from custody, and they subsequently made their way to the new Mormon settlement in
Hancock County, Illinois, where Joseph Smith was
killed in 1844. In Doniphan's honor, Joseph and Emma Hale Smith named a son
Alexander Hale Smith. In 1843,
Porter Rockwell, a controversial Mormon figure later known as "the destroying angel of Mormondom", was arrested in
St. Louis and accused of carrying out a failed assassination attempt on (now former) governor Boggs. After nine months of being imprisoned in poor conditions, he was able to hire Doniphan to defend him; Doniphan managed to have the main charge of attempted murder dismissed for lack of evidence, and arranged for Rockwell to serve a five-minute sentence (for a jailbreak attempt during his imprisonment) in the county jail before being released. Rockwell made his way to Illinois, then later to Utah, where he achieved fame as a lawman and
Wild West figure. Forty years after the events of 1838, an aged Doniphan visited
Salt Lake City, Utah Territory, which had become the nucleus for
the largest body of Mormons following the death of Joseph Smith. He received a hero's welcome, and was feted and thanked by the Latter-day Saints for his role in saving the life of their prophet. ==Mexican–American War==