The player's goal in HISTORY Civil War: Secret Missions is to disrupt the armies of both the North and the South by any means necessary, including conducting train raids, stealing ironclad ships, stopping enemy supply lines, destroying enemy artillery and more. All events are drawn from the real life actions of famous partisans, scouts and rangers – fight as a member of Mosby's Rangers, Sheridan's Scouts and Grant's Secret Service and receive your mission commands from famous generals including Robert E. Lee, "Stonewall" Jackson, and Ulysses Grant.
The action in HISTORY Civil War: Secret Mission accurately reflects the guerrilla tactics of the time period. Weapons include the shotgun, the pepperbox revolver and the coffee mill gun, and there is heavy reliance on scouts and naval warfare.