By early 1838 conflicts had arisen between Smith and Cowdery.
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Leadership. Cowdery competed with Smith for leadership of the new church and "disagreed with the Prophet's economic and political program and sought a personal financial independence [from the] Zion society that Joseph Smith envisioned."
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Church and state. In March 1838, Smith and Rigdon moved to Far West, which had been under the presidency of Cowdery's brothers-in-law,
David and John Whitmer. There they took charge of the Missouri church and initiated a number of policies that Cowdery and the Whitmers believed violated separation of church and state.
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Personal Behavior. In January 1838, Cowdery wrote his brother Warren that he and Joseph Smith had "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." Alger, a teenage maid living with the Smiths, may have been Joseph Smith's first
plural wife, a practice that Cowdery opposed.
On
April 12, 1838, a church court excommunicated Cowdery after he failed to appear at a hearing on his membership and sent a letter resigning from the Church instead. The Whitmers,
William Wines Phelps and Book of Mormon witness
Hiram Page were also excommunicated from the church at the same time..
Cowdery and the Whitmers became known as "the dissenters," but they continued to live in and around Far West, where they owned a great deal of property. On
June 17, 1838, President
Sidney Rigdon announced to a large Mormon congregation that the dissenters were "as salt that had lost its savor" and that it was the duty of the faithful to cast the dissenters out "to be trodden beneath the feet of men." Cowdery and the Whitmers took this
Salt Sermon, and its implicit endorsement of the "
Danites, a secret vigilante group, as a threat against their lives and fled the county. Reports of their treatment circulated in nearby non-Mormon communities and increased the tension that led to the
Mormon War.