Lee was born in Illinois Territory, and joined the Church of Jesus Christ of Latter-day Saints (LDS Church) in 1838. He was a close friend of Joseph Smith, Jr founder of the LDS Church. Lee practiced plural marriage and had at least eighteen wives and sixty children. Lee was allegedly a member of the Danites, although some have argued there is little or no evidence for his involvement in the group.
After Smith's murder, Lee joined the bulk of the LDS Church's members in establishing a new community in what is now Utah.
In 1856, Lee became a U.S. Indian Agent in the Iron County area, assigned to help Native Americans establish farms.
In September, 1857, a group traveling from Arkansas was attacked in a four-day seige dubbed the Mountain Meadows Massacre. Lee was among the attack's leaders, in which at least 120 people were killed.
After the killings, Lee remained active in Mormonism and local government. In the late 1860s, however, various questions arose publicly about the exact nature of the massacre. Lee was excommunicated from the LDS Church in 1870 for his part in the massacre.
In 1872 Lee moved from Iron County and established a ferry crossing on the Colorado River.
Lee was arrested in 1874, tried and sentenced to death for leading the massacre. He never denied his own complicity, but stated he was a scapegoat meant to draw attention away from other Mormon leaders also involved.
On March 23, 1877, Lee was executed by firing squad, on the site of the 1857 massacre.
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