By 1844, the conflict between the Mormons in Nauvoo and their Illinois neighbors was reaching a breaking point, but more concerning to the Prophet was the threat of apostates inside the Church. "All the enemies upon the face of the earth may roar and exert all their power to bring about my death," said Smith, "but they can accomplish nothing, unless some who are among us join with our enemies, and bring their united vengeance upon our heads"
But the number of Church members who opposed plural marriage—and other newly revealed doctrines—was growing. William Law, the second counselor in the Church's First Presidency, met with other Church leaders who all believed that Smith was a fallen prophet. Their followers numbered about 200 during the early months of 1844. They made plans to denounce Smith at the Church's conference in April.
Their plans were thwarted, however, when the conspirators were outed by the Church's official newspaper, and the men were summarily excommunicated. In response, Law and others established what they deemed a Reformed Church that rejected plural marriage. They established an opposition newspaper in Nauvoo, and its first edition was printed on June 7, accusing the prophet of preaching polytheism, practicing whoredoms and spiritual wifery, and blaspheming God.
The next day the Nauvoo city council met and ruled that this opposition paper was a "public nuisance" because it slandered Church leaders—and if allowed to continue, would stir up mob action against the citizens of Nauvoo. Mayor Joseph Smith then ordered the city marshal to destroy the paper's printing press, scatter the type, and burn all copies of its newspapers.
The destruction of the press and razing of the printing office prompted calls from citizens of nearby towns for the arrest of Smith and other Church leaders, and the removal of all Mormons from Illinois. "War and extermination is inevitable! Citizens arise, one and all!" wrote Thomas Sharp in his newspaper. "Can you stand by, and suffer such infernal devils to rob men of their property and rights without avenging them?" Anti-Mormon sentiment increased the following week when Smith was brought before a Nauvoo municipal court and quickly released.
Acting as both Mayor of Nauvoo and leader of the Nauvoo Legion, the prophet put the city under martial law on June 18. Anticipating mob action, he appealed to Illinois governor Thomas Ford for military assistance. Governor Ford wrote an open letter calling for calm on both sides, but also wrote privately to the prophet, insisting that the public would not be satisfied unless Smith and other city council members stood trial before a non-Mormon judge in nearby Carthage.
Smith conferred with Church leaders, and told them that since it was only himself and his brother Hyrum that the mob wanted brought to justice, it was clear what he must do. The Holy Spirit had told him to secretly cross the Mississippi with Hyrum that night and flee to the West to live among the Natives. And so they bid farewell to their families, and with the help of Porter Rockwell and Willard Richards, made the river crossing on June 22.
The next morning a posse arrived to arrest Joseph and Hyrum Smith, and threatened that unless they were turned over, the city would be invaded by troops. This news was brought to the prophet—as well as word that his fleeing was considered by many to be cowardice. "What shall I do?" Smith asked his friend Porter Rockwell. "You are the oldest and ought to know best," replied Rockwell. "And as you make your bed, I will lie with you."
"If my life is of no value to my friends, it is of none to myself," resolved the prophet in deciding to return to Nauvoo. Earlier in the year, Smith had gathered the Twelve Apostles. Prophesying his own death, he put all the powers of the priesthood in their hands such that they could continue the leadership of the Church in his absence. Now Smith spent the evening with his family, knowing it would likely be the last time he saw them.