Upon hearing about the death of Joseph Smith, Miller returned to Nauvoo. A succession crisis ensued whereby a variety of men vied for the leadership of the Latter Day Saints. The majority of Latter Day Saints accepted the leadership of Brigham Young and the Quorum of the Twelve, and Miller provided lukewarm support for this decision. Because he was one of two bishops in the church, Miller was appointed by Young to be a legal trustee-in-trust for the church on August 9, 1844, Miller was sustained as the president of Nauvoo high priests quorum and the "Second Bishop of the Church" on October 7, 1844. In 1845, Miller submitted to Young a proposal to construct a building for the high priests quorum in Nauvoo. Young, who by then had plans to lead the Latter Day Saints away from Nauvoo, rejected Miller's plan outright. This signalled the start of cool relations between Miller and Young which eventually led to Miller's abandonment of the organization led by Young. Although Miller left Nauvoo under Young's instructions in 1846, and came as far as Winter Quarters, Nebraska, Miller informed Young in January 1847 that he would not follow him to the Salt Lake Valley, as Young had planned. Rather, Miller accepted the leadership claims of apostleLyman Wight and emigrated with Wight and his followers to the Republic of Texas. Brigham Young disfellowshipped Miller from the church on December 3, 1848, but he was never formally excommunicated from The Church of Jesus Christ of Latter-day Saints.
Later life
By 1849, Miller had become convinced that Lyman Wight and his "Wightite" church were apostate. He became convinced that James J. Strang was the true successor to Joseph Smith, and, in 1849 he left, to join Strang's followers in Wisconsin. Miller arrived in Voree, Wisconsin, on September 4, 1850, and shortly thereafter moved with Strang and his followers to Beaver Island, Michigan. In Beaver Island, he was an active member of Strang's Church of Jesus Christ of Latter Day Saints. When Strang was assassinated in 1856, Miller left Beaver Island with the other departing "Strangites". Miller died in the second half of 1856 in Marengo, Illinois; he was en route to California at the time.
Marriages
Miller's first wife, Mary Fry, was sealed to him in the Nauvoo Temple on 13 January 1846. Miller practiced plural marriage, and he was sealed to Elizabeth Bouton and Sophia Wallace on January 25, 1846.
Status in LDS Church: Presiding Bishop?
There is debate as to whether Miller should today be accepted as a former presiding bishop of The Church of Jesus Christ of Latter-day Saints. The office of presiding bishop was not established as such in the church until the tenure of Edward Hunter. Nevertheless, Edward Partridge, the first bishop of the Latter Day Saint movement, is usually regarded as the first presiding bishop of the LDS Church. On the same day that Miller was sustained as the "Second Bishop" of the church, Newel K. Whitney—who was the second ordained bishop in church history—was sustained as the "First Bishop" of the church; therefore, Whitney is usually recognized by the LDS Church as the de facto presiding bishop until his death in 1850, with Miller as a subordinate or assistant to Whitney until his break with the LDS Church in 1848.