 He fought and was wounded at the Battle of Liberty, but returned to fight at the Battle of Shiloh, where he was taken prisoner.Stone was paroled by Jefferson Davis and sent to Washington, D.C. to negotiate an exchange of prisoners; after initially failing to reach an agreement, he returned to Confederate captivity, was again paroled, and was released after an exchange agreement was reached.In 1862, Stone was promoted to colonel of the 22nd Iowa Volunteer Infantry Regiment.