President Abraham Lincoln placed Connor in charge of the 3rd California Volunteer Infantry at the outbreak of the American Civil War in 1861. Fearing that the Confederates would try to isolate the newly formed state of California from the rest of the Union, Lincoln ordered Connor and his men to Salt Lake City to protect the overland mail routes from Indian attack. Incensed by this assignment, Connor pleaded with his superior officers to allow him to take his men east to fight in the main theater of the Civil War. He argued that the men under his command wanted to "serve their country in shooting traitors instead of eating rations and freezing to death around sage brush fires..." They longed for “the privilege of going to the Potomac and getting shot." His request denied, he stayed in Utah Territory to protect the mail routes. He ordered his men to construct Fort Douglas in Salt Lake City.
After two years without any military action, Connor instigated an opportunity to fight. The Northwestern Shoshone periodically traded with emigrant parties on the Oregon Trail, one of the primary routes under Connor’s protection, or defended themselves against unscrupulous miners traveling between Utah Territory and the future states of Idaho and Montana. Mormon settlement in Utah Territory and increased traffic along the Oregon Trail limited the resources available to the Northwestern Shoshone. By the 1860s, the Shoshones had few choices but to exact a toll from emigrants and settlers utilizing Indian resources without compensating the tribe. Northwestern Shoshone warriors attacked a group of eight miners early in January 1863, killing two of them. The survivors made their way to Salt Lake City where they testified to Chief Justice John F. Kinney that Shoshones had attacked them. Kinney issued a warrant for the arrest of several Indian chiefs from the Northwestern Shoshone tribe including chiefs Bear Hunter, Sagwitch, and Sanpitch. The territorial marshal, Isaac L. Gibbs, recognizing that he would not be able to pursue and arrest the Shoshone chiefs by himself, requested the aid of Connor and his men. Connor accepted enthusiastically.
Connor made it abundantly clear that because his superiors denied him the chance to fight Confederates in the South, he intended to fight Indian warriors instead. “Connor anticipated that a major fight with the Indians would give his bored troops an opportunity to exhibit their fighting prowess and might gain him new and more exciting appointments.” He later admitted, “it was not my intention to take any prisoners.” His expedition had nothing to do with protecting the overland mail routes, or arresting the Shoshone chiefs--he simply wanted a chance to fight but instead orchestrated a massacre.