Set during the mid-1990s, Rokuro "Rock" Okajima(you) is a 25-year-old Japanese salaryman working for Asahi Industries in Tokyo. One day, he is taken hostage by the crew of the Elco-type PT boat Black Lagoon, the Lagoon Company, a group of pirate mercenaries dedicated to smuggling goods in and around the seas of Southeast Asia. The group is composed of Dutch, the African-American leader and a former U.S. Navy patrol boat crewman; Revy, the Chinese-American main gunfighter of the team; and Benny, a Jewish-American college dropout, who serves as the mechanic, computer specialist, and researcher.

After his department chief abandons Rock, declaring him dead, he decides to join the crew. Despite living now as a pirate, Rock retains his skills and good-natured attitude, serving the team as their negotiator and "professional" face of the group. The crew's base of operations is located in the fictional town of Roanapur, Thailand, which is home to pirates, thieves and various criminal organizations, including the Japanese yakuza, the Chinese triad, the Russian and Italian mafias and the Colombian cartel. The Lagoon Company takes on a variety of missions, which generally involve violent gunfights and wars with all kind of criminals.