As arrests grew, hundreds of “cohabs” were languishing in various penitentiaries from Detroit Michigan to Salt Lake City. Most of the leaders then decided to go underground to avoid the posses that were searching for them. In many cases this meant that Polygamist men and women were shuttled from place to place, sent messages via code and generally kept in hiding. Some members of the leadership, such as George Q. Cannon and Joseph F. Smith were sent to other countries to avoid the law, Cannon to Mexico, Smith to the Sandwich Islands (Hawaii).LDS leaders felt they were secure in their own belief that they were not going against the constitution, no matter what laws and courts said. These leaders believed they had answered most of the accusations of the anti-polygamists who believed that women were being conned into being plural wives and forced into staying with these husbands. Moreover they were trying to gain sympathy by allowing the media to play up the imprisonment of their leaders and others following polygamy. However, just as the Mormons had not listened to the seriousness of the rulings and laws brought against them by their opponents, the other side did not care if the facts did not meet the reality. The truth was, when the anti-polygamists realized that the women in polygamous relationships were not willing to immediately rat out their husbands or to flee from US marshals it was apparent to some that they were not the innocents that some thought they were.
So as Edmunds and others in the Senate and Congress looked for new ways to enforce the removal of Polygamy they saw that their older moral ideas would not work. Edmunds saw this early on, he was convinced that he had to break up the power structure of the church by taking away their political rights. As Senator, Edmunds had been a nominee for President at the 1880 convention which after a vicious political battle elected James A. Garfield the Republican candidate for, and eventual, President of the United States. He would also be a candidate in 1884 losing again. Edmunds was considered a part of the reformist camp that wanted to change the way politics worked.  In an era of Robber Barons and monopolists Edmunds considered the Church of Jesus Christ of Latter-day Saints the biggest Robber Baron of them all.
When the Edmunds-Tucker Act of 1887 went into effect it was aimed at two things, one of which was the ability of women in polygamous marriages to escape punishment. The second one was to target the ability of the Church to maintain its financial position. The act took on the perceived monopoly of the Church by taking away its right to hold property, fund emigration of Mormons from abroad, and took away the last piece of its political power by revoking the rights of Utah women to vote. It was the harsh hammer, which people like the Utah anti-polygamists, and Edmunds wanted, to finally defeat the Church.
The LDS Church leaders, under the direction of a new President, Wilford Woodruff, were seeing their plural wives being arrested and charged with fornication. 200 women were arrested, some because they were pregnant, for having children of polygamists. It turned plural wives into prostitutes under the law. The second major problem for the church was they were decertified as a corporation and no longer allowed to possess land with a value of over $50,000. This put in jeopardy all the temples the church had built in Logan, St. George, Manti and the unfinished main one in Salt Lake City all of which were in Utah. If the church lost its financial resources it would make it impossible for them to carry on their ecclesiastical missions across the world or to help new converts immigrate to Utah. Woodruff and a majority of the other leaders felt they had few options. In 1890 the Supreme Court once again ruled against the Church in the Late Corporation of the Church of Jesus Christ of Latter-day Saints v. United States. The court upheld the seizure of Church property ending the last hope. At last the Mormons understood that they had to take a different tack than hoping their problems would go away, they had to proactively choose a new path.
Until the 1980s one other aspect of the historiography of the polygamist era which has been covered is one of the more controversial. Church history after 1890, both official and otherwise, move from the polygamy period to discussing the modernization of the church. However, Michael Quinn, a former professor at Brigham Young University, in 1985 article brought up the reality that polygamy did not cease amongst the church leaders. Since his writings a number of others have discussed this period.
In September of 1890 the Church announced a new policy, called a Manifesto. Woodruff would now use this document to claim that the church would now follow the laws of the land and give up on plural marriage. However, this was not the only thing the church did it also saw that it needed to change its relationship with the Republican party who had run the federal government of the United States almost exclusively since 1860. The church sought to build a relationship with the Republicans, with firebrand reformers like Edmunds now out of the Senate, and much of the fury dissipated by the Manifesto the Republicans saw an opportunity to gain a large voting bloc in the West. Through this mutual benefit Utah achieved statehood in 1896 finally and completely gaining control over marriage within the state. Edmunds overall desire to reduce the political influence of the church in Utah had failed.
The historiography of the period has also changed over time, from general histories to micro history. Much of the new history is hard to classify in schools other than New Mormon History, which was self classified. Since much of the history of the period has for the most part only happened since the 1980s it would be obvious that much of the weight of the studies would fall into the synergist school.
The confrontation over polygamy was one where populists, evangelists, and politicians saw their ability to control federal politics had risen to its zenith, a number of historians feel that their goals in Utah matched a larger goal to reform American society into one which their own Protestant Christian, and rural values dominated. It lasted only a few years but it had a large effect on society as whole and Mormons in particular. After 1890 the Church no longer openly supported plural marriage, but they did not disavow it completely, to the surprise of some and the shock of thousands in 1904, it was revealed that the church had not ended the Principle. It just divested itself of the responsibility of protecting polygamists from the law. Only after Joseph F. Smith, the new President of the church announced a second Manifesto, one that included church discipline for practicing plural marriage, did the church actively end the practice.
After ten years of legal and political warfare, the Mormons and the anti-polygamist reformers only really understood one another at the end when both sides had exhausted themselves. For most of the period they spent it talking past one another. While in reality it would be sixteen years before the LDS church would be considered finished with polygamy, after yet another confrontation between the two forces, after 1890 much of the power of polygamy was finished. As confrontation turned to cooperation Americans focused on the actions of the Mormon church only ever flared up in very rare instances. Modern Mormonism would change into a much more generally accepted monogamist religion at the same time as the political influence of Evangelical Christianity started to wane.
 Gustive O. Larson, The “Americanization” of Utah for Statehood, (San Marino, CA: Huntington Library), 1971, 145-151.
 Allan Peskin, “Who Were the Stalwarts? Who Were Their Rivals? Republican Factions in the Gilded Age,” Political Science Quarterly, Vol. 99, No. 4. (Winter, 1984-1985), 708.
 Gordon, 202-203
 Gordon, 207-208
 Kathleen Flake, The Politics of American Religious Identity: The Seating of Senator Reed Smoot, Mormon Apostle, (Chapel Hill, NC: University of North Carolina Press), 2004, 30.
 Kathleen Flake, and Richard Van Wagoner among others.
 Flake 46-49.
 Flake, 51-52.