The Mormons, now under the leadership of Brigham Young, went out to Utah to establish their own kingdom. In what felt like the relative safety of the intermountain West, Mormons began to practice plural marriage in the open — and ended up paying dearly for this lapse in secrecy.

In 1856 the Republican Party made the defeat of polygamy a key plank in its first national platform, characterizing it alongside slavery as one of the "twin relics of barbarism." The federal government soon criminalized the practice and then in effect outlawed membership in the Mormon Church until it would agree to give up polygamy. And after the Civil War, federal prosecutors convicted and jailed thousands of Mormons in the most coordinated campaign of religious repression in U.S. history.

The reaction of the Mormon Church to this new wave of persecution was, initially, to take refuge in secrecy once again. In 1890, the president of the church, Wilford Woodruff, issued a manifesto in which he gave his "advice" to members of the Mormon Church not to enter into any marital relationships that would violate the laws of the land. But like Jewish rituals under the Spanish Inquisition, plural marriage continued, secretly in Utah and also among refugees, who fled to Mexico or other places the law could not reach.

Matters came to a head when another apostle, Reed Smoot, was elected in 1903 to the U.S. Senate as a Republican from Utah, despite political opposition from President Theodore Roosevelt. Opponents of Mormonism, mostly Protestants, sought to block Smoot from taking his seat.

Over several years, the Senate engaged in a series of hearings that put Mormonism on trial. The president of the church, Joseph F. Smith, a nephew of the founding Smith, was called to testify and sought somewhat unsuccessfully to conceal both the continuing practice of plural marriage as well as his own status as seer and revelator. After returning to Utah, Smith issued a manifesto of his own, in 1904, aimed at ending plural marriage.

After that, plural marriage gradually disappeared from the mainstream Mormon scene until it remained only among peripheral fundamentalist or sectarian Mormons who defied the church authorities. In 1907, the Senate finally voted to seat Smoot. The course was set for the Mormon religious practice of the 20th century: a process of mainstreaming, both political and theological.

The less said the better about the particular teachings of the church, including such practices as the baptism of the dead and the doctrine of the perfectibility of mankind into divine form. Mormons depicted themselves as yet another Christian denomination alongside various other Protestant denominations that prevailed throughout the United States.

In politics, Joseph Smith was something of a radical. He preached, instead of democracy, a version of theocratic rule within a framework given by his own prophetic leadership.