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.

The main character Rokuro Okajima is meek, mudane, and metropolitan. His business trip to South East Asia turns from pleasure cruise to festival of pain when modern day pirates board the ship and take him hostage. Revy, Dutch, and Benny are merciless, maniacal and mean. Together, they makeup the crew of the Black Lagoon. Making a living in a city where the most villanious of villains make themselves at home isnt without its risks, but they take on any job available to them: smuggling guns, drugs, kidnapped children, and stolen goods is all part of a hard days work for this crew.