In 1864, Jefferson Davis asked Thompson to lead a delegation to Canada, where he appears to have been leader of the Confederate Secret Service.

Union troops burned down his mansion in Oxford, Mississippi, the hometown of William Faulkner, who based some of his fictional characters on Thompson.

He was admitted to the bar in 1834 and established a law practice in Pontotoc, Mississippi in 1837, and made an unsuccessful bid to become the state attorney general.

He denounced Republicans in the North who spoke of the slavery issue as an "irrepressible conflict" and Southern extremists who favored reopening the Atlantic slave trade.

"Secretary Thompson has entered openly into the secession service, while professing still to serve the Federal authority," the New York Times reported on December 20.

When he resigned, Horace Greeley's New-York Daily Tribune denounced him as "a traitor", remarking, "Undertaking to overthrow the Government of which you are a sworn minister may be in accordance with the ideas of cotton-growing chivalry, but to common men cannot be made to appear creditable.

[citation needed] He attained the rank of lieutenant colonel and was present at several other battles in the Western Theater of the war, including Corinth, Vicksburg, and Tupelo.

From there, he directed a failed plot to free Confederate prisoners of war on Johnson's Island, off Sandusky, Ohio, in September.

[8] According to the testimony of the Peace Democrat Clement Vallandigham, Hunt met Thompson, talked to him about creating a Northwestern Confederacy, and obtained money for arms, which was routed to a subordinate.

[9] One plot was a planned burning of New York City on November 25, 1864 in retaliation for Union Generals Philip Sheridan and William Tecumseh Sherman's scorched-earth tactics in the South.