By early 1838, the relationship between Smith and Cowdery had deteriorated significantly. Cowdery felt that Smith's integration of economic and political plans into his theology and ecclesiastical structure was encroaching on the
separation of church and state. Cowdery also expressed his concerns of Smith's relationship with
Fanny Alger, a teenage maid living with the Smiths in Kirtland. In a January 1838 letter to his brother
Warren: "[We] had some conversation in which in every instance I did not fail to affirm that which I had said was strictly true. A dirty, nasty, filthy affair of his and
Fanny Alger's was talked over in which I strictly declared that I had never deserted from the truth in the matter, and as I supposed was admitted by himself." Nine excommunication charges were presented against Cowdery, which included selling lands in Jackson County without authorization, trying to destroy the character of Joseph Smith, and disregarding his ecclesiastical duties for the practice of law. On April 12, 1838, a church court excommunicated Cowdery. David Whitmer was also excommunicated at the same time, and apostle
Lyman E. Johnson was disfellowshipped; John Whitmer and Phelps had been excommunicated a month earlier. Cowdery refused to appear before the council, but sent a letter of resignation, reiterating his desire to live his religious beliefs independent from his economic and political decisions. These men became collectively known as "dissenters", but continued to live in and around Far West, where they owned a great deal of property, much of which was purchased when they were acting as agents for the church. Possession became unclear and the dissenters threatened the church with lawsuits. After Rigdon delivered
a sermon that implied dissenters had no place in the Latter Day Saint community, a vigilante group called the
Danites forcibly expelled them from the county. The
Danite Manifesto, a letter addressed to Cowdery and the other dissenters, was signed by some eighty-four Latter-Day Saints (but not Smith or Rigdon). It warned: you shall have three days after you receive this communication to you, including twenty-four hours in each day, for you to depart with your families peaceably; which you may do undisturbed by any person; but in that time, if you do not depart, we will use the means in our power to cause you to depart. Cowdery and the dissenters fled the county. Reports about their treatment circulated in nearby non-Mormon communities and increased the tension that led to the
1838 Mormon War, which ultimately resulted in the Latter-Day Saints' expulsion from Missouri.
Post-excommunication period (1838–48) Between 1838 and 1848, Cowdery studied and practiced law in
Tiffin, Ohio, where he became a civic and political leader. He joined the local
Methodist church and served as secretary in 1844. He also edited the local
Democratic newspaper until it was learned that he was one of the Three Witnesses, at which time he was reassigned as assistant editor. He was nominated as his district's Democratic Party candidate for the
Ohio State Senate in 1846, but was defeated when his Mormon background was discovered. After the
Smiths’ death on June 27, 1844, a
succession crisis split the Latter Day Saint movement. Cowdery's father and brother were followers of
James J. Strang, who pressed his claim as the movement's successor by claiming that he had found and translated ancient records engraved upon
metal plates, similar to the golden plates Smith had translated in the 1820s. In 1847, Cowdery and his brother moved to
Elkhorn,
Wisconsin, about twelve miles away from Strang's headquarters in
Voree. In Elkhorn he entered law practice with his brother and became co-editor of the
Walworth County Democrat. In 1848 he ran for state assemblyman but was again defeated when his Mormon ties were disclosed. == LDS Church rebaptism ==