On New Year's Eve 1958, Hyman Roth celebrates his birthday and the expansion of the Corleone family into Cuba. However, "la revolucion" breaks out, and Michael Corleone manages to escape with most of the other family members. Aldo Trapani, the main protagonist in The Godfather II , is killed, and five new families threaten the Corleone family's control over New York, Florida, and Las Vegas. As Aldo Trapani's closest soldier, Dominic takes on his role to help Michael and the Corleone family win the war and build a new family. As Dominic, the player moves freely through three cities: New York, Florida, and Cuba, traveling between them by airplane. The main goal is to grow Dominic's family and destroy the other five families. This is done in two main steps: taking over businesses and killing "Made Man". Taking over a business involves entering the shop, fighting through enemy guards, and finding the person with the Godfather-sign over their head. Each business owner has a weak spot and a breaking point. A weak spot can be exploited by destroying inventory or intimidating them, giving a 25% bonus on monetary outcome. However, if pressured too much, they may become aggressive and attack without mercy. Intimidation is successful if the player gains control of the business, and they receive a one-time cash advance and daily money.
The player also controls crime rings, which provide bonuses for taking over them. However, these bonuses can be lost if the player loses one of the rackets in the ring. The enemy families do not sit back and let Dominic take their businesses one by one, so the player must hire guards to protect them.
The player can hire soldiers, known as "Made Man", who have specializations. As the player progresses, they can promote some of these soldiers to learn new professions. The player can also upgrade certain skills, such as Survival, for a fee. If a Made Man is downed by enemy fire, there is a time window to revive them with adrenaline.
Favors are handed out by random people and high-ranking officials, providing the player with missions that involve killing or beating up enemies. These favors can be saved for later use, allowing the player to rebuild businesses.
The game features a multiplayer mode that ties in with the single-player campaign. The player chooses one of their hired family members and takes on their role in four game modes: Team Deathmatch, Demolition Assault, FireStarter, and Safecracker. The player earns honor points for their family member, which can be used to buy new weapon licenses.