Because of Indian troubles and the extreme isolation of Clarkston, all the settlers in the spring of 1866 moved to Smithfield, Logan and other parts of the valley. Some left the valley entirely.

When the settlers expressed a desire to return to their homes in Clarkston in the spring of 1867, Brigham Young advised them that they might do so if they built a fort and a public corral for protection of the livestock. This was done. Houses were built in the form of a fort extending along both sides of the present Main Street, and a public corral was provided.

The existence of the Clarkston settlement was threatened in 1869 when a majority of the settlers, due mainly to discouragement because of the severe winters and heavy drifting snow, decided to move to the present site of Newton. But a few people decided to stay in Clarkston and some who had left returned, and the settlement became a permanent one. There was a controversy over retaining the name Clarkston for the original settlement or transferring it to the "New Town."