As a soldier in either the Union or Confederate armies, the player is involved in covert operations behind enemy lines. The eleven missions in this game are inspired by events that took place during the American Civil War.
The player's goal is to disrupt the armies of both the North and South by any means necessary, including stopping enemy supply lines, stealing ironclad ships and sabotaging enemy strongholds. Engaging in some of the Civil War's most famous battles, such as The Great Train Raid of 1861 and The Fall of Vicksburg, the gamer will utilize classic weapons of the era, including the Pepperbox Revolver and the Coffe Mill Gun.
All missions are based on the actions of famous partisans, scouts and rangers – fighting as a member of Mosby's Rangers, Sheridan's Scouts and Grant's Secret Service and receiving mission commands from famous generals like Robert E. Lee, "Stonewall" Jackson, and Ulysses Grant.
The game takes the player through secret missions that took place on both sides of the war. The player has to battle enemy forces and protect his fellow soldiers. Melee is a large part of the game, as it was in the prequel. Reload times vary from weapon to weapon, with muskets taking a long time to reload, and repeating rifles taking a relatively short time.
Missions includes being a part of a secret sniper mission at the Battle of Gettysburg, conducting a covert train raid on the B&O Railroad, sabotaging artillery outposts during the Lewisburg Deception, and many more. The player will be equipped with the weaponry and military advancements of the Civil War such as the automatic guns of the era and the usage of repeating rifles, grenades, sabers, exploding artillery, and shotguns.
The game features intense, tactical combat. It's based on authentic Civil War combat methods, artillery barrages, urban assaults, sniping, and stealth.
Bonus objectives are thrown at you from mission to mission like saving P.O.W.s and destroying crates. Players can ignore and accept these mission. Each level begins with a documentary video describing every mission and the importance it played in the Civil War.
The game encompasses eleven missions, all of which are seen from the perspective of either a Northern or Southern soldier.
- Dawn At Chancellorsville (CSA)
- Dr. Gatling's Secret Weapon (CSA)
- The Gray Ghost (CSA)
- Sharpshooters at Devil's Den (CSA)
- The Great Train Raid of 1861 (CSA)
- USS Pittsburg (USA)
- Sabotage at Lynchburg (USA)
- Infiltration of Jackson (USA)
- Captain Blazer's Scouts (USA)
- The Siege of Vicksburg (USA)
- The Fall of Vicksburg (USA)
Among many famous commanders who participated in the Civil War, the player will also encounter fellow footsoldiers with varying abilities and personalities. Some historical figures making an appearance in the game include:
- General Robert E. Lee
- General "Stonewall" Jackson
- General Ulysses S. Grant
The two main factions in the game are the conflicting sides of the Civil War. The player will have a chance to enlist in the armies of both the Confederacy and the Union, with missions, allies, and enemies varying depending upon the character's alliegance.
A varying arsenal of weaponry is available to the player. All are period arms that would have been seen in the hands of actual participants in the war. A full list of firearms and melee weapons in shown below:
- Colt Army Model 1860
- Remmington Model 1858
- Allen & Thurber Pepperbox
- Sharps 1855
- Colt Model 1855
- Spencer 1860 Carbine
- Henry 1860
- Whitworth Rifle
- Double-barreled Shotgun
- Gatling Gun
- Coffee Mill Gun
- Bowie Knife
Civil War: Secret Missions features many collectibles and hidden items found throughout the various levels. These range from letters and journal pages written by both Northern and Southern soldiers, to Photographs of historic locations and individuals.