With the outbreak of the American Civil War in 1861, Stone enlisted in the Confederate army that April. He commanded Company K of the Second Mississippi Infantry and saw action in Virginia. Stone, who had the rank of colonel, in 1862 was placed in command of another regiment due to a reorganization in 1862. Colonel Stone was highly commended by his division commander Maj. Gen. Henry Heth and in 1864 he frequently commanded the brigade. In January 1865 he went recruiting in Mississippi and then commanded local defense troops countering Stoneman's Raid. He and his men were captured in North Carolina and held prisoner in Camp Chase, Ohio; later being transferred to Johnson's Island, Ohio.
Political career
At the end of the war, Stone returned to Tishomingo County. He was elected mayor and treasurer. In 1869, he won a race to become state senator, winning re-election in 1873. State elections were marked by fraud and violence; the Red Shirts, a paramilitary group, worked to disrupt and suppress black voting, and turned Republicans out of office. After Governor Adelbert Ames resigned in 1876, Stone, who was President Pro Tempore of the Mississippi Senate at that time, served as the acting governor. In the 1877 election, Stone won the Governor's office in his own right, as a Democrat; in 1881 he was defeated for re-election by Robert Lowry. Stone became Governor again after winning the 1889 election. The gubernatorial term was extended through 1896 by the new state constitution of 1890. Determined to keep control and maintain white supremacy, the Democratic-dominated legislature effectively disfranchised most African Americans in the state by adding a requirement to the constitution for voter registration for payment of poll taxes. Two years later, they passed laws requiring literacy tests, and grandfather clauses. These requirements, with additions in legislation of 1892, resulted in a 90% reduction in the number of blacks who voted in Mississippi. In every county a handful of prominent black ministers and local leaders were allowed to vote. African Americans were essentially excluded from the political system for 70 years, until after passage of federal civil rights legislation in the mid-1960s. When this constitution and laws survived an appeal to the US Supreme Court, other southern states quickly adopted the "Mississippi Plan" and passed their own disfranchising constitutions, through 1908. Voter rolls dropped dramatically in other southern states as well, and politics was dominated by white Democrats.
After the war, Stone married Mary G. Coman in 1872. The couple had two children who died young. They adopted three children of John's brother and raised them as their own.
The John M. Stone Cotton Mill in Starkville was formerly named in his honor, but it was renamed after being purchased by Mississippi State University in 1962. This building was used to house the university police department, but it has since been demolished.
