In his report, Major Carleton wondered whether it would be possible to administer justice in this case.

"In pursuing the bloody thread which runs throughout this picture of sad realities, the question how this crime, that for hellish atrocity has no parallel in our history, can be adequately punished often comes up and seeks in vain for an answer," he wrote.

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Carleton then addressed the truly responsible parties with the anger that only a person who saw the remnants of the massacre could muster.

"But how inadequate would be the punishment of a few, even by death, for this crime for which nearly the whole Mormon population, from Brigham Young down, were more or less instrumental in perpetrating," he wrote.

John Lee was identified very early on as the best scapegoat. He had been with the Indians at the beginning of the massacre, had persuaded the Gentiles to surrender their arms, and several witnesses had spoken about the gusto with which he undertook the mission of slaying the immigrants. By 1859, with a federal warrant out for his arrest, he was clearly a liability for the Church and despite his close ties to Young, was quickly exiled to the remotest part of the Mormon empire and subsequently excommunicated. When he was no longer useful to Brigham Young, the Prophet saw to it that he was disposed of.

Still, Lee was not arrested by federal agents until 1874. He was put on trial before a jury of three Gentiles, one Apostate Mormon and eight Saints. After a month-long trial, Lee's jury announced it was hopelessly deadlocked and a mistrial was declared. The prosecutor "lost an unwinnable trial, but in the process he destroyed Mormonism's public image in the court of public opinion," Will Bagely wrote. "He inflicted wounds on the Mormon theocracy that would never heal."

The federal officials quickly moved for a second trial, this time offering Lee his freedom if he would testify against the Church hierarchy. Lee declined. This time, other participants came forward and testified against him. The Church had turned against John Lee, and he was sacrificed in hopes that his punishment would close the matter. He was quickly convicted and sentenced to die. He was given a choice of hanging,  firing squad,  or beheading, which served the need for blood atonement. While awaiting his execution, he penned his scathing Confession (although many believe it was ghostwritten or even completely fabricated). Nonetheless, Lee's Confession is widely used by historians investigating Mountain Meadows. As if to show his contempt for his Mormon brothers who had cast him out, Lee opted for the firing squad. On March 21, 1877, John Lee was executed by federal troops near Mountain Meadows, the scene of his crime. No one else was ever tried for the crimes at Mountain Meadows.

In September 1999, near the site of the Massacre, families of both the killers and the victims met to remember the terrible events of 142 years prior. Brigham Young's successor, President Gordon B. Hinckley, spoke to the crowd. "I come as a peacemaker," he said. "This is not a time for recrimination or the assigning of blame...It is time to leave the entire matter in the hands of God."

Then, bearing in mind that God might forgive, but the lawyers for the families of the victims might not, Hinckley added, "That which we have done here must never be construed as an acknowledgement of the part of the church in any complicity in the occurrences of that fateful day."