Thompson was never a full Confederate General, but he became well-known as the "Swamp Fox of the Confederacy." In August 1863, he was captured in Pocahontas, Arkansas. He was held at Fort Delaware until his release in early 1864. Returning to the West, he participated in the Missouri raid conducted by Gen. Sterling Price. He was put in command of the Confederate "Iron Brigade," formerly led by Brigadier General Joseph Shelby. He served in this capacity until May 1865, when he was forced to surrender over 5,000 troops at Jacksonport.
