Rokurou "Rock" Okajima has joined the Lagoon Company, a pirate mercenary group which operates out of Roanapur, Thailand. Despite his initial protests, this filthy slum of depraved souls and merciless criminals now serves as the former salaryman's home. Stranded, with nothing left of his past life but the clothes on his back and his inner morality, Rock is forced to perform jobs alongside the other members of the Lagoon crew. Berated for his lack of spine as he wades through the underbelly of society, he must decide whether to continue on amidst the gunfire and ruthlessness or risk everything he has in an attempt to be free. Whether he chooses the comfort of a familiar land or the freedom of being an outlaw, his decision will have lasting consequences on the crew who gave him a home.

Within Thailand is Roanapur, a depraved, crime-ridden city where not even the authorities or churches are untouched by the claws of corruption. A haven for convicts and degenerates alike, the city is notorious for being the center of illegal activities and operations, often fueled by local crime syndicates. Enter Rokurou Okajima, an average Japanese businessman who has been living a dull and monotonous life, when he finally gets his chance for a change of pace with a delivery trip to Southeast Asia. His business trip swiftly goes downhill as Rokurou is captured by a mercenary group operating in Roanapur, called Black Lagoon. The group plans to use him as a bargaining chip in negotiations which ultimately failed. Now abandoned and betrayed by his former employer, Rokurou decides to join Black Lagoon. In order to survive, he must quickly adapt to his new environment and prepare himself for the bloodshed and tribulation to come. A non-stop, high-octane thriller, Black Lagoon delves into the depths of human morality and virtue. Witness Rokurou struggling to keep his values and philosophies intact as he slowly transforms from businessman to ruthless mercenary.

Special omake episodes from the Blu-Ray releases, showing the heroines and foes in funny, uncommon situations.

When Sanpeita Kobayashi was a child, his lovely friend had to move away, but she vowed that in ten years, they would meet again—as husband and wife. Ten years later, Sanpeita is a high school student, but he hasn't forgotten the feelings they shared. Sanpeita awakes from a dream about his last day with her, only to have his morning interrupted. A weird robot girl is battling other robots in his bedroom, claiming to be his wife. The robot's pilot looks like none other than Sanpeita's long-lost, childhood friend. But who is she really? Why did she have to leave? And what does she have to do with the Mishima Electronics Corporation?