Palmer was incarcerated at the notorious Castle Thunder prison on Tobacco Row, Richmond where his true identity was never uncovered. Doubts about his identity were apparently reinforced by publication of a fictitious dispatch in the Philadelphia newspapers that purported that Palmer was in Washington, D.C. after scouting in Virginia. When he was freed after four months of confinement, he found that his guide, the Reverend J.J. Stine, had escaped but been arrested by Union authorities, accused of betraying him to the enemy. Rather than risk Palmer's life by publication of the circumstances in the Northern press, Stine had remained imprisoned in Fort Delaware until Palmer's personal application to Secretary of War Edwin Stanton resulted in his release.