Second year high school student Koguma doesn't lead a very interesting life. She has no parents, and no friends nor hobbies to keep her daily life busy. One day, she acquires a second-hand Honda Super Cub motorcycle and rides it to school. As time goes by, not only does Koguma have a new adventurous life, but she also forges precious friendships thanks to her precious little motorcycle.

This is a story of connecting shining emotions. Joy, sadness, anger. Feelings are a power, invisible to the eye, that every person possesses. Sometimes this power is even capable of changing the world. Hiori Hirahara always has a positive attitude and can't leave people in trouble alone. Ruki Hanari is socially awkward, she wants to get along well with others, but she doesn't know how to go about it. How will the meeting of these two wildly different girls change not only them, but the world itself?

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.