On 13 April 1838, JS participated in a meeting that the and held to consider the charges against and . Johnson had begun challenging JS’s leadership by May 1837, when he and fellow filed charges with , accusing JS of “lying & misrepresentation— also for extortion— and for— speaking disrespectfully against his brethren behind their backs.” The next month, Johnson and his fellow apostle and business partner, , sought to dissuade apostle from accepting a missionary appointment to . In a 3 September 1837 conference, Johnson, his brother , and Boynton were rejected as apostles because of their opposition to the . The three men reconciled with the church a week later at another conference and were reinstated as apostles. Shortly afterward Johnson traveled with to . While there, Johnson attended the November church conference, during which he was again sustained as an apostle. However, by December, Johnson was meeting with Cowdery, David and , and other dissenters in to discuss their opposition to other church leaders. Johnson seems to have associated especially with Cowdery, and the two apparently planned to start a legal practice together. In January 1838, Johnson attended a meeting with Cowdery, the Whitmer brothers, and other dissenters, during which they made plans to leave Far West because of their opposition to the high council there. Johnson also continued to correspond with and other , Ohio, dissenters. On 7 April 1838, apostle reported at a church conference that he could not sustain Johnson and four other members of the . Two days later, church leaders wrote to Johnson, Cowdery, and David Whitmer, reporting that charges had been made against them and that hearings would be held on 12 April for Cowdery and on 13 April for Johnson and Whitmer.

Neither nor attended the 13 April hearing, during which the high council and the presidency investigated the charges against the two men. Instead, like the day before, Johnson and Whitmer sent letters expressing their opposition to the charges and the council proceedings and indicating they were withdrawing from the church. The council deliberated over Johnson’s case during two sessions, with JS testifying against Johnson during the first session. As a result of the testimony JS and others offered, the council excommunicated Johnson.

The council then turned to the case of . After he, , and had been removed from the presidency in February 1838, the three men had decried the decision. In a 10 March letter, the men argued that the procedures for removing them were “contrary to the principles of the revelations of Jesus Christ, and his gospel.” Later in the day, the high council read the letter and excommunicated Phelps and John Whitmer. No action was taken against David Whitmer until 9 April, when he was notified of his 13 April trial. During the trial, the council read the letter and determined that he should be excommunicated. As the final item of business during the meeting, the council revoked Cowdery’s November 1837 assignment to help identify locations for new Latter-day Saint settlements.

Minutes of the council meeting were taken by the high council clerk, . The minutes were copied into Minute Book 2 by in 1842 or 1843.