During the year, emigrant trains continued to arrive. Some of them were nearly destitute and the fort had to give them supplies. Sometimes troops rode out to rescue stranded emigrants. One train had been attacked and robbed by Indians and Officer Blake sent 11 men to rescue them. Twenty of the original 54 emigrants had been killed. These troubles resulted in 1862, to increasing the fort to 200 soldiers.
The citizens of Virginia City and Carson City were still worried about secessionist problems. There were a few people who were arrested for making what was felt to be treasonable statements. P.H. Clayton was one such man and he was confined at Fort Churchill for three weeks as punishment. In 1863, the Civil War was continuing and more troops were being withdrawn from the West to go east. When the government recruited members for the war department, the Nevada volunteers met at Fort Churchill.
There was additional conflict with the Indians over the cutting of pine trees for building. The pine trees were the source of pinyon nuts, essential for the Indian diet. Fortunately catastrophe was averted most times with negotiation and giving of gifts. In 1864, there was a complaint from Unionville that Paiutes were stealing horses and cattle. Thirty men left the fort to negotiate with the Indians. They never did find any Indians.
In 1864, soldiers from the fort were sent to Virginia City because citizens were worried about the southern sympathizers there. There was also a disturbance in Dayton when a man was lynched, but by the time troops arrived all was quiet. During the summer, there was a problem with the local miner's union when mine owners reduced the daily wage. Fearful of riots, the troops were once again called in to keep the peace.
