Lewis and Elizabeth's real estate valued at $2250 and their personal estate at $650. Their son, daughter-in-law, and grandson were living with them, and they were living next door to Lewis' brother, Byrd Allen, and his family.

Mormons arrived at the Muddy in January 1865 and established St. Thomas; six months later a second group founded St. Joseph nine miles to the north. Both discovered ample evidence that local Paiutes were growing crops along the Muddy River, yet the settlers saw nothing wrong with expropriating the Native Americans' property. It was the Paiute practice to plant corn, beans, squash, and wheat before migrating to the cooler uplands for gathering and hunting. They returned every fall to harvest surviving crops. Needless to say, their 1865 return was an unhappy one.

Not surprisingly, "Indian troubles" soon became a problem for the Muddy Valley settlements. Anger over losing their farm land as well as their belief in sharing resources prompted some Paiutes to appropriate Mormon animals and foodstuffs. Unwilling to admit they had pushed members of the tribe into food destitution, the Mormons called the Paiutes' behavior "theft" and "beggary," often responding by punishing "offenders." The Paiutes sometimes reciprocated with violence.

In addition to difficulties with Native Americans, the Muddy Valley Mormons faced severe environmental and climatic conditions. As the Muddy's source was a mineral spring, it was salty and unsuitable for large-scale irrigation agriculture. Searing heat in the summer and frequent bouts of drought tested the settlers. Man-made disasters also posed challenges. On August 18, 1868, the second St. Joseph burned down after two young boys lost control of a fire while roasting potatoes.

Many Mormon families simply could not endure the Muddy Mission's extreme hardships and left. To determine whether the settlements could survive, Brigham Young visited in March 1870. He was not hopeful. That fall, a flood wiped out the new Muddy village of West Point.

The final straw, however, came during a fight over taxes. In 1870, a new boundary survey confirmed that the Muddy settlements were in Nevada, not in Utah or Arizona. Both of those territories had accepted taxes in the form of goods, but Nevada officials wanted back taxes paid in gold or silver. Few settlers could afford this, so in early 1871 all but one Mormon family left the Muddy Mission for good.