After the Civil War began in 1861, the demand for horses increased and Anderson transitioned from trading horses to stealing them, reselling them as far away as New Mexico.
He worked with his brother Jim, their friend Lee Griffith and several accomplices strung along the Santa Fe Trail.
In late 1861, Anderson traveled south with Jim and Judge Baker in an apparent attempt to join the Confederate Army.
Anderson had stated to a neighbor that he sought to fight for financial reasons rather than out of loyalty to the Confederacy.
However, the group was attacked by the Union's 6th Regiment Kansas Volunteer Cavalry in Vernon County, Missouri; the cavalry likely assumed they were Confederate guerrillas.
The Anderson brothers escaped, but Baker was captured and spent four months in prison before returning to Kansas, professing loyalty to the Union.
One way that he sought to prove that loyalty was by severing his ties with Anderson's sister Mary, his former lover.

Upon his return to Kansas, Anderson continued horse trafficking, but ranchers in the area soon became aware of his operations.
In May 1862, Judge Baker issued an arrest warrant for Griffith, whom Anderson helped hide.
Some local citizens suspected that the Anderson family was assisting Griffith and traveled to their house to confront the elder William Anderson.
After hearing their accusations against his sons, he was incensed—he found Baker's involvement particularly infuriating.
The next day, the elder Anderson traveled to the Council Grove courthouse with a gun, intending to force Baker to withdraw the warrant.
As he entered the building he was restrained by a constable and fatally shot by Baker.
The younger Anderson buried his father and was subsequently arrested for assisting Griffith.
However, he was quickly released owing to a problem with the warrant, and fled to Agnes City, fearing that he would be lynched.
There he met Baker, who temporarily placated him by providing a lawyer.
Anderson remained in Agnes City until he learned that Baker would not be charged, as the judge's claim of self-defense had been accepted by legal authorities.
Anderson was outraged and went to Missouri with his siblings.
William and Jim Anderson then traveled southwest of Kansas City, robbing travelers to support themselves.

On July 2, 1862, William and Jim Anderson returned to Council Grove and sent an accomplice to Baker's house claiming to be a traveler seeking supplies.
Baker and his brother-in-law brought the man to a store, where they were ambushed by the Anderson brothers.
After a brief gunfight, Baker and his brother-in-law fled into the store's basement.
The Andersons barricaded the door to the basement and lit the store on fire, killing Baker and his brother-in-law.
They also burnt Baker's home and stole two of his horses before returning to Missouri on the Santa Fe Trail.

William and Jim Anderson soon formed a gang with a man named Bill Reed; in February 1863, the Lexington Weekly Union recorded that Reed was the leader of the gang.
William Quantrill, a Confederate guerrilla leader, later claimed to have encountered Reed's company in July and rebuked them for robbing Confederate sympathizers; in their biography of Anderson, Albert Castel and Tom Goodrich speculate that this rebuke may have resulted in a deep resentment of Quantrill by Anderson.
Anderson and his gang subsequently traveled east of Jackson County, Missouri, avoiding territory where Quantrill operated and continuing to support themselves by robbery.
They also attacked Union soldiers, killing seven by early 1863.
After the Civil War began in 1861, the demand for horses increased and Anderson transitioned from trading horses to stealing them, reselling them as far away as New Mexico. He worked with his brother Jim, their friend Lee Griffith and several accomplices strung along the Santa Fe Trail. In late 1861, Anderson traveled south with Jim and Judge Baker in an apparent attempt to join the Confederate Army. Anderson had stated to a neighbor that he sought to fight for financial reasons rather than out of loyalty to the Confederacy. However, the group was attacked by the Union's 6th Regiment Kansas Volunteer Cavalry in Vernon County, Missouri; the cavalry likely assumed they were Confederate guerrillas. The Anderson brothers escaped, but Baker was captured and spent four months in prison before returning to Kansas, professing loyalty to the Union. One way that he sought to prove that loyalty was by severing his ties with Anderson's sister Mary, his former lover.
Upon his return to Kansas, Anderson continued horse trafficking, but ranchers in the area soon became aware of his operations. In May 1862, Judge Baker issued an arrest warrant for Griffith, whom Anderson helped hide. Some local citizens suspected that the Anderson family was assisting Griffith and traveled to their house to confront the elder William Anderson. After hearing their accusations against his sons, he was incensed—he found Baker's involvement particularly infuriating. The next day, the elder Anderson traveled to the Council Grove courthouse with a gun, intending to force Baker to withdraw the warrant. As he entered the building he was restrained by a constable and fatally shot by Baker. The younger Anderson buried his father and was subsequently arrested for assisting Griffith. However, he was quickly released owing to a problem with the warrant, and fled to Agnes City, fearing that he would be lynched. There he met Baker, who temporarily placated him by providing a lawyer. Anderson remained in Agnes City until he learned that Baker would not be charged, as the judge's claim of self-defense had been accepted by legal authorities. Anderson was outraged and went to Missouri with his siblings. William and Jim Anderson then traveled southwest of Kansas City, robbing travelers to support themselves.
On July 2, 1862, William and Jim Anderson returned to Council Grove and sent an accomplice to Baker's house claiming to be a traveler seeking supplies. Baker and his brother-in-law brought the man to a store, where they were ambushed by the Anderson brothers. After a brief gunfight, Baker and his brother-in-law fled into the store's basement. The Andersons barricaded the door to the basement and lit the store on fire, killing Baker and his brother-in-law. They also burnt Baker's home and stole two of his horses before returning to Missouri on the Santa Fe Trail.
William and Jim Anderson soon formed a gang with a man named Bill Reed; in February 1863, the Lexington Weekly Union recorded that Reed was the leader of the gang. William Quantrill, a Confederate guerrilla leader, later claimed to have encountered Reed's company in July and rebuked them for robbing Confederate sympathizers; in their biography of Anderson, Albert Castel and Tom Goodrich speculate that this rebuke may have resulted in a deep resentment of Quantrill by Anderson. Anderson and his gang subsequently traveled east of Jackson County, Missouri, avoiding territory where Quantrill operated and continuing to support themselves by robbery. They also attacked Union soldiers, killing seven by early 1863.
William T. Anderson