Early in the war, Ferguson organized a guerrilla company and began attacking any civilians that he believed supported the Union. Many local vendettas were prosecuted in occupied Tennessee under the guise of war. His men cooperated with Confederate military units led by Brig. Gen. John Hunt Morgan and Maj. Gen. Joseph Wheeler when they were in the area and some evidence indicates that Morgan commissioned Ferguson as a captain of partisan rangers. Ferguson's men were seldom subject to military discipline and often violated the normal rules of war.