Dwyer began his work as a historian of the American west at the Catholic University of America, in Washington, D.C. in 1938, receiving his Ph.D. in history in 1941. His dissertation was published as "The Gentile Comes to Utah: A Study in Religious and Social Conflict (1862-1890)" and is considered an accomplished and objective work on the religious history of early Utah. Dwyer described Mormonism as an attempt to resurrect the idea of creating an ideal human order on earth. Sections of this work addressed the conflicts between the religious stance of Brigham Young, President of The Church of Jesus Christ of Latter-day Saints and the antipolygamy crusade launched by the federal government (The Gentile Comes to Utah, p. 97, Topping, p. 40).