A team of pirate mercenaries known as the Lagoon Company smuggles goods in and around the seas of Southeast Asia in the early to mid 1990s. The Lagoon Company consists of four members: Dutch, the leader; Revy, the main gunfighter; Benny, the mechanic, computer specialist, and researcher; and you, an ex-salaryman hijacked by the team and abandoned by your department chief, eventually becoming their negotiator and "professional" face of the group, retaining his old job skills.

Their base of operations is located in the fictional harbor city of Roanapur in east Thailand near the border of Cambodia (somewhere in the Mueang Trat district, likely on the mainland north/northeast of the Ko Chang island or on the island itself). The city is home to the Chinese triad, the Russian Bratva, the Colombian cartel, the Italian mafia, a wide assortment of pickpockets, thugs, mercenaries, thieves, prostitutes, assassins, and gunmen. The city also has a large Vietnamese refugee population following the Vietnamese refugees exodus after the communist takeover of Vietnam in 1975. Lagoon Company transports goods for various clients in the American made 80-foot (24 m) Elco-type PT boat, Black Lagoon. It 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, even going as far as Isabela, Basilan in the Philippines. When they are not working, the members of the Lagoon Company spend much of their down time at The Yellow Flag, a bar in Roanapur which is often destroyed in firefights.