Thompson sided with the Confederacy and resigned as Interior Secretary in January 1861. 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. Thompson became Inspector General of the Confederate States Army.
Though not a military man, Thompson later joined the army as an officer and served as an aide to General P. Beauregard at the Battle of Shiloh. He attained the rank of lieutenant colonel and was present at several other battles in the Western Theater of the war, including Vicksburg, Corinth, and Tupelo. In March 1864, Jefferson Davis asked Thompson to lead a secret delegation in Canada.
He accepted and arrived in Montreal in May of that year. Thompson appears to have been the leader of Confederate Secret Service operations in Canada. From there, he directed a failed plot to free Confederate prisoners of war on Johnson's Island, off Sandusky, Ohio, in September.
Regarded in the North as a schemer and conspirator, many devious plots were associated with his name, though much of this may have been public hysteria. On June 13, 1864, Thompson met with former New York governor Washington Hunt at Niagara Falls. 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. Some speculate that John Wilkes Booth, who assassinated Abraham Lincoln, met with Thompson, but this has not been proven. Thompson worked hard to clear his name of involvement in the assassination in the years after the war. His manor, called "Home Place", in Oxford, Mississippi was burned down by Union troops in 1864. The item "Civil War CDV of Confederate Secret Agent and Spy Jacob Thompson Rare" is in sale since Sunday, January 07, 2018. This item is in the category "Collectibles\Militaria\Civil War (1861-65)\Original Period Items\Photographs".The seller is "civil_war_photos" and is located in Midland, Michigan. This item can be shipped worldwide.