日本，在旭日重工工作的普通员工冈岛绿郎。在向客户运送光盘的旅途中，被黑礁商会所捕捉，在不懂翻译的过程中被诱拐。他们的目标是绿郎带的光盘。在陌生地登陆的冈岛绿郎，和三个人一起被卷入了意外的袭击中…。

袭击黑礁商会的是被称为“战争屋”的佣兵们。冈岛绿郎得知自己是公司为了隐瞒事实而被公司抛弃的。被雇佣兵们乘坐的战斗直升机追击到海湾内，在被逼绝境之时洛克有了反击的想法。

在洛克击败了“战争屋”后，正式加入黑礁商会。然后，作为交涉的角色，在进行了暂时的工作的某一天，在罗亚纳普拉的街上，在办公室里享受了一点休息的拉拉斯商会，收到了领取横领品的委托。但是，委托是在俄罗斯黑手党身边工作的人的圈套……。

在战争结束前的印度洋，由联合军击沉的一艘轮船。在那个战舰内，留下了一幅“被布莱斯希尔德引导，十二名骑士”的绘画。黑礁商会的这次工作要打捞那幅画。于是开始进行回收工作的黑礁商会开始了打捞工作。

侵入轮船舰内的洛克和莱薇。另一方面，达奇询问了突然攻击的船舶的情况。他们的目的和他们一样，好像是沉没的轮船的探索，在潜水时进入了降温作业。这样下去会和舰内的黑礁商会碰面。

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.

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.