The pursuit of the perpetrators of the Mountain Meadows massacre, which atrocity occurred September 11, 1857, had to await the conclusion of the American Civil War to begin in earnest.

Brigham Young's involvement

Evidence as to whether or not Brigham Young ordered the attack on the migrant column is conflicted.  Historians still debate the autonomy and precise roles of local Cedar City LDS church officials in ordering the massacre and Young's concealing of evidence in its aftermath. Young's use of inflammatory and violent language in response to the  Federal  expedition added to the tense atmosphere at the time of the attack. After the massacre, Young stated in public forums that God had taken vengeance on the Baker–Fancher party. It is unclear whether Young held this view because he believed this specific group posed an actual threat to colonists or were directly responsible for past crimes against Mormons. According to historian MacKinnon, "After the war, Buchanan implied that face-to-face communications with Brigham Young might have averted the Utah War, and Young argued that a north-south telegraph line in Utah could have prevented the Mountain Meadows Massacre."

Young's belated message to Isaac C. Haight, acting commander of the Iron Brigade
On September 8, 1857, Capt. Stewart Van Vliet of the U.S. Army Quartermaster Corps arrived in Salt Lake City. Van Vliet's mission was to inform Young that the United States troops then approaching Utah did not intend to attack the Mormons, but intended to establish an army base near Salt Lake, and to request Young's cooperation in procuring supplies for the army. Young informed Van Vliet that he was skeptical that the army's intentions were peaceful, and that the Mormons intended to resist occupation.

On September 10, 1857, James Holt 
Haslam arrived in Salt Lake City, after experiencing long delays during his nearly 300 mile journey, to deliver a  message from the acting commander of the Iron Brigade, Isaac C. Haight to the Mormon leader Brigham Young.  The letter has yet to be found.

President Young's message of reply to Haight, dated September 10, read: "In regard to emigration trains passing through our settlements, we must not interfere with them until they are first notified to keep away. You must not meddle with them. The Indians we expect will do as they please but you should try and preserve good feelings with them. There are no other trains going south that I know of[.] [I]f those who are there will leave let them go in peace."

Yet, by the time the express rider delivered Young's letter to Haight, ordering that the emigrants not be harmed, the murders at Mountain Meadows had already taken place. According to trial testimony given later by express rider Haslam, when Haight read Young's words, he sobbed like a child and could manage only the words, "Too late, too late."

Historians debate the letter's contents. Brooks believes it shows  Young "did not order the massacre, and would have prevented it if he could." Bagley argues that the letter covertly gave other instructions.

Part played by Paiutes
A few days after the massacre, September 29, 1857, John D. Lee briefed Brigham Young on the massacre. According to Lee, more than one hundred and fifty "mob members" of Missouri and Illinois, with many cattle and horses, damned the Saints leaders, and poisoned not only a beef given to the Native Americans, but also a spring which killed both Saints and Native Americans. The Native Americans became enraged and after a long siege killed everyone and stripped the corpses of clothing. The Mormons spared eight to ten children. A second group, with a large cattle herd, would have suffered the same fate had not the Saints intervened and saved them. Wilford Woodruff recorded Lee's account as a "tale of blood."

In fact, seventeen children had survived. The names and ages are recorded in the Carleton report, available online. The Mormons sold the children among each other, as they did the material goods they stole from the emigrants. Carleton reported that immediately after the massacre John D. Lee, Haight, and Philip Smith [Klingonsmith] went to Salt Lake City to ask Brigham Young what should be done with the property. They offered Young the money they had taken from their victims, but he  would have nothing to do with it. Brigham gave Lee instructions to divide the cattle and cows among the poor, and left it to him to distribute it as he chose. John D. Lee ended up owning a fancy carriage that had been part of the column; the wagons, rifles and other valuables ended up with the Mormons, which the Paiute pointed out was proof that they had not perpetrated the massacre. Other emigrant property was auctioned in Cedar City, in the tithing office of the church, where the Mormons termed it, facetiously, in Carleton's view, "property taken at the siege of Sebastapol."

On September 30, 1857, Mormon Indian Agent George W. Armstrong sent a letter to Young from Provo with information of the massacre. In his account, the emigrants gave the Native Americans poisoned beef. After many Native Americans died, they "appeased their savage vengeance" by killing fifty-seven men and nine women. There was no mention of survivors.

Decades later, Young's son, 13 years old in 1857, said he was in the office during that meeting and that he remembered Lee blaming the massacre on the Native Americans. Some time after Lee's meeting with Young, Jacob Hamblin said he reported to Young and George A. Smith what he said Lee had related to Hamblin on his journey to Salt Lake. Brigham Young was mistaken when he later testified, under oath, that the meeting took place "some two of three months after the massacre". When Lee attempted to relate the details of the massacre, however, Young later testified he cut Lee off, stopping him from reciting further details.

Rumors of the massacre began to reach California in early October. John Aiken, a "gentile" who traveled with the mail carrier John Hurt through the killing field, reported to the Los Angeles Star that the unburied putrefied corpses of the women and children were more generally eaten than the men.

Confirmation of the massacre was received from the Mormon J. Ward Christian. Christian claimed that the emigrants had cheated the Native Americans who sold them wheat at Corn Creek, put strychnine in water holes and poisoned a dead ox. According to Christian, the party consisted of 130 to 135. All were killed by Native Americans with the exception of fifteen infant children, that have since been purchased with much difficulty by the Mormon interpreters.

And when Brigham Young sent his report to the Commissioner of Indian Affairs in 1858, he said the massacre was the work of Native Americans.

Paiute leaders maintain that Mormon accounts of Paiute initiation of the siege are untrue. Stoffle and Evans assert that Paiutes had no history of attacking wagon trains and no Native Americans were charged, prosecuted, or punished by federal officials as a result of the Mountain Meadows massacre. Tribal oral history accounts taken in 1980s and 1990s relate stories of Paiutes witnessing the attack from a distance rather than participating. There are some stories, which relate some Paiute were present, but did not initiate or participate in the killings. A corroborating oral history of Sybil Mariah Frink tells of witnessing the planning of the massacre at her home in Harmony. She contends she followed fourteen Mormons who had disguised themselves as Native Americans to the scene of the massacre. She makes no mention of any Native Americans participating in the attack. Authors Tom and Holt summarize the state of proof regarding the massacre:
The fact that so much evidence, including relevant pages from the journals of many settlers, has been lost or destroyed, testifies to many Native Americans and their sympathizers that much of the official history cannot be considered to be complete or truthful. However, there is certainly some evidence that Native Americans with base camps on the Muddy and Santa Clara Rivers were at least involved in the initial siege of the wagon train."

While Native American Paiutes were present, certainly during the initial attack and siege, historical reports of their numbers and the details of their participation are contradictory. However, Mormon witnesses of the event are unreliable, as Carleton demonstrates, and were attempting to shift the blame onto the Native Americans.

Eyewitness accounts from Mormons that implicate the Paiutes (at first entirely so and then only in part) are set against Paiute accounts that absolve them from participation in the actual massacre. Historian Bagley believes "the problem with trying to tell the story of Mountain Meadows—the sources are all fouled up. You've either got to rely on the testimony of the murderers or of the surviving children. And so what we know about the actual massacre is—could be challenged on almost any point. _ " However, as Carleton mentions in his 1857 report, even Hamblin, the Indian agent who blamed the Paiutes for the massacre, admitted to him that in 1856 the Paiute tribe had only three guns, suggesting that it was incredible for them to have acquired sufficient guns to inflict the number of gunshot wounds evident among the victims, most of whom were killed by gunfire, not, as Mormon witnesses claimed, largely by being hit in the head with stones.

Orchestration by militia
Although militia members put responsibility on the Natives, many non