The plot follows a team of mercenaries known as Lagoon Company, who smuggle goods in and around the seas of Southeast Asia. Their base of operations is located in the fictional city of Roanapur in Thailand, and they transport goods in the PT boat Black Lagoon. Lagoon Company does business with various clients, but has a particularly friendly relationship with the Russian crime syndicate Hotel Moscow. The team takes on a variety of missions - which may involve violent firefights, hand-to-hand combat, and nautical battles - in various Southeast Asian locations and when not doing much, the members of the Lagoon Company spend much of their down time at The Yellow Flag, a bar in Roanapur.