"Black Lagoon" is set in the early 1990s and revolves around the criminal underworld of Southeast Asia, particularly in the fictional city of Roanapur, Thailand. The narrative centers on Rokurou Okajima, a Japanese salaryman who is kidnapped by the mercenary group known as the Lagoon Company during a business trip. After his employer abandons him, Rokurou, now nicknamed "Rock," chooses to join the Lagoon Company, abandoning his former life. The group operates as a transport and smuggling outfit, taking on dangerous jobs for various criminal organizations.

The Lagoon Company consists of several key members: Revy, a skilled and ruthless gunfighter with a troubled past; Dutch, the composed and strategic leader of the group; and Benny, a tech-savvy former college student who handles logistics and communications. Together, they navigate the treacherous waters of Roanapur, a city controlled by rival gangs, mafias, and corrupt officials. The series explores their interactions with various factions, including the Russian mafia, the Colombian cartel, and the Triad, as well as their involvement in high-stakes missions that often blur the lines between morality and survival.

Revy serves as Rock's primary foil, embodying the harsh realities of the criminal world, while Rock retains a sense of idealism and moral ambiguity. Their dynamic evolves as Rock becomes more entrenched in the group's operations, grappling with the ethical dilemmas of his new life. The series delves into themes of loyalty, identity, and the consequences of violence, often presenting morally complex situations without clear resolutions.

Episodic arcs introduce a range of characters, such as Balalaika, the enigmatic leader of the Russian crime syndicate Hotel Moscow, and Roberta, a former revolutionary turned deadly bodyguard. These characters add depth to the narrative, showcasing the interconnectedness of Roanapur's criminal underworld. The series balances intense action sequences with character-driven moments, exploring the psychological toll of living in a lawless environment.

"Black Lagoon" is notable for its gritty portrayal of crime and its exploration of the human condition within extreme circumstances. The story maintains a fast-paced, episodic structure, with each arc contributing to the overarching narrative of survival and adaptation in a world where trust is scarce and danger is constant. The series does not shy away from depicting the brutality of its setting, offering a raw and unflinching look at the lives of those who operate on the fringes of society.