[3] Alcorn was a delegate to the special Mississippi convention of 1851 called by Democratic governor John A. Quitman, who, as an opponent of Henry Clay's Compromise of 1850 advocated secession.

Like many other Whig planters, Alcorn opposed secession, pleading with the secessionists to reflect on the realities of the national balance of power.

[3] Alcorn, during the war, was in uniform for about eighteen months of inconspicuous field service, mainly in raising troops and in garrison duty.

At the start of the Civil War, Alcorn was ordered to proceed with his troops to central Kentucky; then, he was stationed at Fort Donelson, Tennessee.

In October 1861, Alcorn raised three regiments of militia troops, designated as the Army of 10,000, committed to sixty days of service in Mississippi and led his brigade to Camp Beauregard, Kentucky, at which he served under General Leonidas Polk.

Additionally, in 1863 his plantation was raided by General Leonard Ross' troops during the Yazoo Pass Expedition, part of the Vicksburg Campaign.

His older son, James Lusk Alcorn Jr., committed suicide in 1879 after returning home from the war partially deaf and a drunkard.

An inscription on the monument at the family cemetery attributes James' death to the "insane war of rebellion" (apparently his father's words).

Seventeen-year-old Henry "Hal" Alcorn ran away during the war to join the military against his father's wishes, became ill, and was left behind and captured.

Alcorn became the leader of the scalawags, who comprised about a fourth of the Republican officials in the state, in coalition with carpetbaggers, African-Americans who had been free before the outbreak of the Civil War, and freedmen.

His hostility to a state civil rights bill was well known; so was his unwillingness to appoint local black officers where a white alternative could be found.

One complained that Alcorn's policy was to see "the old civilization of the South modernized" rather than lead a total political, social, and economic revolution.

[18] Alcorn's estrangement from Senator Adelbert Ames, his northern-born colleague, deepened in 1871, as African-Americans became convinced that the former governor was not taking the problem of white terrorism seriously enough.

Alcorn resisted federal action to suppress the Ku Klux Klan, instead contending that state authorities were sufficient to handle the task.

Ames was supported by the Radicals and most African Americans, while Alcorn won the votes of most of the scalawags, moderately Whiggish whites.

In 1875, when Reconstruction was fighting for its life against a campaign of violence from the Democrats, Alcorn emerged and led a white force against black Republicans at Friar's Point.

In his later life, Alcorn practiced law in Friars Point, Mississippi, and lived quietly at his home, Eagle's Nest, in Coahoma County.