Baker served with the Confederate Army during the American Civil War, joining shortly after his second marriage. It is claimed he shot and killed at least three African Americans, killing a black woman in an immigrant train and later shooting a black boy six times with a pistol after taking the Oath of Allegiance and becoming an overseer of Freemen. By 1864 he had either been discharged or deserted, and he joined a group called the "Independent Rangers", loosely associated with the Confederate Home Guard. It was intended to pursue and capture deserters from the Confederate Army, but more often than not took advantage of most of the men being away at war, leaving mostly elderly men, women and children. This left the door open for acts of intimidation, rape, theft and violence for groups of well-armed men like the "Independent Rangers". Shortly after Baker joined the "Independent Rangers" they began an ongoing feud with another band called the "Mountain Boomers", but by the end of that year the "Boomers" had been driven out or forced to disperse due to several of their members having been killed by the "Rangers". In November, 1864 Baker led a group of "Rangers" to intercept a band of Arkansas settlers, mostly older men, women and children who had fled Perry County, Arkansas for a better life out West. Allegedly this was considered "un-patriotic" by Baker, but more likely than not is that he wished to rob them of their possessions. The "Rangers" caught up with these fleeing settlers as they were crossing the Saline River somewhere in the Ouachita Mountains, but when the settler band refused to return Baker drew his pistol and shot and killed the band's leader. With assurances from Baker that he would not kill anyone else, the remaining settlers returned to Baker's side of the river, where he quickly led his "Rangers" in shooting and killing nine other men. The event became known locally as the Massacre of Saline.