While on a business trip at sea for his company, Rokuro Okajima is abducted by the members of the Lagoon Company: Dutch, Revy, and Benny. After obtaining a confidential disc for their client, Balalaika, the head of Hotel Moscow and a part of the Russian Mafia, Revy takes Rokuro as a hostage onto their ship, the Black Lagoon, to hold for ransom. Despite this, Rokuro begins to bond with the members of the Lagoon Company, and Dutch gives him the nickname "Rock". Meanwhile, the board of Rock's company gives Kageyama, Rock's superior, the authority to pursue the missing disc, and Kageyama hires a mercenary group to attack the Lagoon Company when they stop in the port city of Roanapur. The group dispatches the majority of the mercenaries and escapes to the Black Lagoon in their car. However, the Lagoon Company is contacted by Kageyama, who informs Rock that he has been declared dead by the company, and shortly afterwards a heavily armed helicopter gunship from the same mercenary group starts chasing the Black Lagoon.
To evade the gunship, Dutch drives the Black Lagoon down a river, but reaches a dead end. Realizing the futility of their situation, the members of the Lagoon Company begin to plan for the worst. Despite this, Rock concocts a plan to defeat the gunship, deducing that the gunship pilot's mentality is akin to that of a duelist, wanting to face their opponent face-to-face. Following Rock's plan, Dutch uses a sunken ship as a springboard to launch the Black Lagoon into the air and destroy the gunship with torpedoes. The Lagoon Company manages to deliver the disk to Balalaika, who gives the disk to Kageyama, as he had made a deal with the Russian Mafia as a contingency. Instead of returning with Kageyama, however, Rock decides to stay with the Lagoon Company, who accept him as a new member.
While staying in Roanapur, where the Lagoon Company is situated, Dutch is accosted by Chin, a gangster who warns Dutch of continuing to work for Balalaika. Dutch ignores his warnings and receives a job from an anonymous employer. As the group leaves on the Black Lagoon, Chin contacts Luak, the head of a pirate gang, to kill the Lagoon Company, and Luak attacks the Black Lagoon with a squadron of boats. Dutch tricks two of the boats into destroying each other via friendly fire, and Revy destroys the rest with an M79 grenade launcher and a PM-63 RAK while leaping from boat to boat. Subsequently, the job is revealed to be a hoax set up by Chin, who is killed by Balalaika.
The Lagoon Company is dispatched to retrieve a painting, The Twelve Knights Led by Brunhilda, from a sunken World War II-era U-boat that left Germany at the eve of Nazi Germany's defeat and was sunk by the United States Navy near Jakarta. Dutch purchases scuba equipment for Rock and Revy to use in retrieving the painting, and Benny instructs the two to enter the submarine via its torpedo tubes and create a hole to exit. After Rock and Revy, with an APS underwater assault rifle, begin descending, the Black Lagoon is attacked by a group of neo-Nazis who fire TOW missiles at the ship.
The Black Lagoon evades the TOW missiles, but Dutch and Benny observe the Nazis send a team underwater to retrieve the painting. Inside the submarine, Rock and Revy locate the painting, but Revy insists on searching the ship for medals and other valuables. When Rock voices his disapproval, Revy asserts that her turbulent childhood pushed her to reject God, love, and other emotions and to believe that everything has no value except for the money it can bring. The two are attacked by the Nazis and in the midst of the firefight, Rock loses the painting. The Nazis obtain it and retreat back to the surface with it. Revy attempts to pursue them, but Rock forces her to abandon the fight when the Nazis use machine guns to fire into the water. Rock and Revy return to the Black Lagoon, where Dutch plans an assault on the Nazis' ship to retrieve the painting.
Dutch and Revy leave the Black Lagoon on a motorboat to raid the Nazis' ship. With the Nazis celebrating their retrieval of the painting, the two easily enter the ship, and Dutch instructs Revy to distract the crew while he searches for the painting. Revy obliges, killing all the Nazis she comes across, but Dutch is forced to stop her when she tries to kill the civilian crew members, which Dutch attributes to Revy's unease at accepting Rock into the crew. Dutch eventually finds Ratchman, the Nazi commander, talking to Sir Alfred, a former Schutzstaffel member that ordered Ratchman to retrieve the painting. Dutch deduces that Alfred hired the Lagoon Company to doubly insure that he would acquire the painting, and Ratchman is furious at this revelation. After Alfred ends the conversation, Dutch and Revy kill Ratchman, finishing their mission.
Megumi Toyoguchi
Revy
Hiroaki Hirata
Benny
Mami Koyama
Balalaika
Tsutomu Isobe
Dutch
Youichi Nishijima
Storm/Stanford