The story follows a team of pirate mercenaries known as the Lagoon Company, that smuggles goods in and around the seas of Southeast Asia in the early to mid 1990s. Their base of operations is located in the fictional harbor city of Roanapur in southeast Thailand near the border of Cambodia.
Abducted by modern-day pirates and declared dead by his company, businessman Rokuro Okajima joins his captors on their ship, the Black Lagoon.
Rock devises a plan to destroy the gunship that seems to have trapped the Black Lagoon. Meanwhile, the Lagoon Company accepts Rock as a new member.
A gangster named Chin lures Dutch and the crew of the Black Lagoon into a battle at sea against Luak, the leader of rival pirates.
While on a mission to retrieve a valuable painting from a sunken U-boat, the Black Lagoon is besieged by missile-firing neo-Nazis.
After finding the painting on the sunken sub, Rock and Revy argue over looking for more loot while the neo-Nazis' own divers approach the wreck.
Dutch and Revy's violent raid on the neo-Nazi ship leads to surprising revelations about Revy and the Black Lagoon's mission to recover the painting.
Revy's resentment at being sent on assignment with Rock may change when he calms a potentially volatile situation with a dealer.
The Black Lagoon crew must deliver a young hostage to a Colombian cartel, but Dutch has a crisis of conscience when he learns the boy's identity.
The Black Lagoon crew discovers too late that Roberta is a formidable opponent with a price on her head, as they attempt to flee with Garcia.
Rock learns the truth about Balalaika's troops when they intervene in a no-holds-barred confrontation between Revy and Roberta.
While transporting information on a terrorist organization to the CIA, the Black Lagoon crew comes under attack by the terrorists.
Rock learns the truth about Takenaka while under interrogation, and gets an even bigger surprise after he's rescued by Revy and Shenhua.
A rash of killings targeting Hotel Moscow prompts a meeting of the major crime lords and suspicion falls on a pair of twin children.
After Rock and Chang trace the twins' origins to Romania, they become engaged in a deadly game of cat-and-mouse with the lethal kids.
Gretel takes Eda hostage, demanding a getaway boat for herself and her brother. Meanwhile, Hansel holds off Balalaika's entire team alone.
The Florida mafia and various bounty hunters descend on the Church of Violence in pursuit of U.S. counterfeiter Greenback Jane, who wants to join.
Eda tries to help Jane evade the bounty hunters, but her plans -- including an escape on the Black Lagoon -- are foiled at virtually every turn.
Dutch and Benny attempt to rescue Jane and the others, and much will be revealed after the chase as they are pursued by the bounty hunters.
Rock and Revy accompany Balalaika to Japan, where they enact -- then endanger -- an assignment to take out one yakuza gang at the behest of another.
Feuding breaks out between Balalaika and the Washimine gang, and Rock makes a shocking discovery about Yukio, the girl he met at the festival.
Yukio is abducted on the day she takes control of the Washimine Group, and Rock pleads with Ginji to let him and Revy help rescue her.
Revy and Ginji try to save Yukio during a battle with Chaka and his men. Later, she takes Rock to task for trying to save her from a life of crime.
Balalaika has wiped out much of the Washimine Group, but Yukio has learned something about Hotel Moscow's technique and uses it to her advantage.
Rock tries to force Yukio out of a life of crime, but events beyond his control may cause his well-laid plans for her future to spin out of control.