The morning began with whiskey. Anderson and roughly 80 guerrillas rode into Centralia dressed in stolen Federal uniforms, an irony that would prove fatal for the engineer of an approaching North Missouri Railroad train. Seeing blue-clad men on the platform, the engineer slowed to a stop. The guerrillas swarmed aboard, separating 125 passengers into civilians and soldiers. Twenty-four Union troops were on the train, all heading home on furlough after fighting at the Battle of Atlanta. Anderson ordered them to strip off their uniforms at gunpoint. The soldiers complied, standing in the September air in their underclothes. Then the shooting began. After the executions, Anderson's men mutilated and scalped the bodies. They torched the depot, set the train ablaze, and sent the burning cars rolling down the tracks toward Sturgeon. Only Sergeant Goodman was spared, taken prisoner for a future exchange that never materialized. He escaped ten days later near Rocheport.

Six hours after the massacre, Major Andrew Vern Emen Johnston rode into Centralia with 146 men of the newly formed 39th Missouri Infantry Regiment. Johnston was a former schoolteacher with limited combat experience, commanding raw recruits armed with single-shot muzzle-loading Enfield rifles. Townspeople warned him that Anderson had at least 80 well-armed men. Johnston pressed on anyway. When he located the guerrilla force, he made a decision that sealed his regiment's fate: he ordered his men to dismount and form a line of battle on foot. Anderson's bushwhackers, each carrying multiple revolvers, charged on horseback. The first Union volley killed several guerrillas, but before the recruits could reload their single-shot weapons, the mounted fighters were among them. Of 147 Federal soldiers, 123 were killed. Only one man was wounded and survived. Confederate losses totaled three dead and ten wounded. According to Frank James, his younger brother Jesse fired the shot that killed Major Johnston.

The Centralia Massacre was not an isolated atrocity but the product of Missouri's vicious internal conflict. By 1864, the Confederacy was crumbling, and General Sterling Price launched a desperate invasion of northern Missouri, hoping to influence the presidential election by capturing St. Louis and Jefferson City. Price actively encouraged guerrilla warfare and railroad disruption. Anderson, who had already earned the sobriquet 'Bloody Bill' through a string of killings across Boone County, was among those who answered the call. Just days before Centralia, his men had killed eleven soldiers and three Black civilian teamsters in a skirmish east of Rocheport. The Federal response was equally brutal: six captured guerrillas were executed at a house in Rocheport the next day. Anderson attacked the town of Fayette on September 24, losing thirteen men. The cycle of reprisal violence had no bottom.

The aftermath was swift and merciless. Brigadier General Clinton B. Fisk wrote to General William Rosecrans suggesting depopulation and devastation of the region as retribution. Anderson himself was killed a month later, on October 27, 1864, in an ambush near Richmond, Missouri. His body was beheaded and his head mounted on a telegraph pole. Jesse James, who had ridden with Anderson at Centralia, would go on to become America's most famous outlaw, robbing banks and trains across the Midwest until his assassination in 1882. Today, the Centralia battlefield sits quietly in rural Boone County. Seventy-nine Federal soldiers killed that day are buried at Jefferson City National Cemetery, their names read each year by those who remember. The town itself, population around 4,000, bears no visible scars of the carnage, though historical markers on the site recall the morning when a train whistle signaled the beginning of one of the Civil War's most lopsided massacres.