When the Civil War started, Connor volunteered for service in the Union army and was appointed Colonel of the Third California Infantry with instructions to guard and secure the overland mail route across the West. In October 1862 he moved his command to Salt Lake City, where he founded Camp Douglas and at once engaged in an acrimonious and bitter cold war with Brigham Young and the Mormon people, whom he accused of being disloyal and immoral. Connor won a brigadier general's star for his destruction of 250 northwestern Shoshoni at Bear River near Franklin, Idaho, on 29 January 1863. In the spring of 1865, he was named commander of the District of the Plains and placed in charge of the Powder River Expedition, whose goal was to pursue and punish the Sioux, Arapaho, and Cheyenne Indians in what is today Wyoming. The expedition was unsuccessful except for a band of Arapaho Connor defeated at Tongue River on 29 August 1865. Connor then returned to the military District of Utah where he was discharged as a Brevet Major-General in the spring of 1866.