Following Morgan's death on September 4, 1864, Clarke formed his own guerrilla band and returned to Kentucky in October.

[3] His raids seemed to inspire the Louisville Journal's stories of the infamous "Sue Mundy", and caused Maj. Gen. Stephen G. Burbridge, military governor of Kentucky, substantial embarrassment.

On the night of February 2, 1865, this joint force of Quantrill and Clarke rode into Lair Station, Kentucky, and burned the railroad depot and freight cars.

A week later on February 8, 1865, the guerrillas killed three soldiers, took four more prisoner and destroyed the remnants of a wagon train.

On March 12, 1865, 50 Union soldiers from the 30th Wisconsin Infantry, under the command of Maj. Cyrus Wilson, who were tasked with capturing Clarke and his gang, surrounded a tobacco barn ten miles south of Brandenburg near Breckinridge County.

Three days after his capture Union authorities scheduled Clarke for public hanging just west of the corner of 18th and Broadway in Louisville.

[5] Clarke's last requests were for his body to be sent to his aunt and stepmother in Franklin to be buried in his Confederate uniform, next to his parents.

"[6] Several thousand people were estimated to have attended Clarke's execution, attracted by rumors that he was "Sue Mundy".

On October 29, 1865, Union authorities hanged Henry Magruder behind the walls of the Louisville Military Prison.