During their winter in Texas, Quantrill's lieutenant, William "Bloody Bill" Anderson, took some of the men to organize his own group.  With two such groups in the area, Texas residents became targets for raids and so many acts of violence that regular Confederate forces had to be assigned to protect residents from the activities of the irregular Confederate forces.

Finally, General McCulloch determined to rid North Texas of Quantrill’s influence and on March 28, 1864 Quantrill was arrested on the charge of ordering the murder of a Confederate Major. However, Quantrill escaped returning to his camp near Sherman, Texas, pursued by over 300 state and Confederate troops. His band then crossed the Red River into Indian Territory, where they resupplied from Confederate stores and started the long journey back to Missouri.

Soon, his guerrilla band began to break up into several smaller units and his vicious lieutenant, "Bloody Bill" Anderson, known for wearing a necklace of Yankee scalps into battle, would continue to terrorize the state of Missouri. As Quantrill’s authority over his followers disintegrated they elected George Todd, a former lieutenant to Quantrill, to lead them.

Anderson's greatest fame came as a result of a massacre and battle with Union soldiers at Centralia, Missouri, when on September 27, 1864, he led a band of about seventy men into the town. Some dressed in captured Union uniforms, the ruffians showed no mercy to the Centralia residents as they systematically raided homes and stores. Barricading a train that approached Centralia, Anderson's men found 23 unarmed Union soldiers on furlough. The soldiers were taken from the train, and ordered to disrobe. After isolating one soldier, Sergeant Tom Goodman, the other 22 soldiers were shot and killed as the horrified Centralia residents and train passengers looked on.

Sergeant Goodman, who was taken hostage by the Anderson guerrillas, lived to write of the whole affair after the Civil War.

William "Bloody Bill" Anderson

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In their final act of wanton destruction, the guerrillas set fire to the Centralia Depot, sacked and set fire to the train and then sent it on its way, west, with no crew aboard, to later crash and be destroyed.

Meanwhile, in an attempt to regain his prestige, Quantrill concocted a plan to lead a company of men to Washington and assassinate President Abraham Lincoln.  He assembled a group of raiders in Lafayette County, Missouri, in November and December 1864 with the idea of completing this task. However, the strength of Union troops east of the Mississippi River convinced him that his plan could not succeed.  Quantrill turned back and resumed his normal pattern of raiding.

With a group of thirty-three men, he entered Kentucky early in 1865. In May a Unionist irregular force surprised his group near Taylorsville, Kentucky, and in the ensuing battle Quantrill was shot through the spine. He died at the military prison at Louisville, Kentucky, on June 6, 1865.  He is buried at the Missouri Confederate Soldier’s Memorial in Higginsville, Missouri.