Salaryman Rokurou Okajima spends his days trying to climb his company's corporate ladder, until one day when a business negotiation in Thailand goes awry. During the botched deal, he falls hostage to the Lagoon Company—a band of ruthless pirate mercenaries. Left to the whims of his captors after his managers refuse to pay his ransom, Rokurou does the unthinkable: instead of begging for his life, he joins the very crew who kidnapped him. Now a member of the group, Rokurou must adjust to his new residence in the dissolute hellscape known as Roanapur, a city where corruption and crime run rampant, and even the smallest slipup could cost him his life. If not for one of the many crime syndicates on the island, Rokurou also constantly finds himself at odds with his brash, gunslinging colleague, Revy. As Rokurou struggles to abandon his past—and with more than just the profits from the Lagoon Company's illegal trading on the line—he must quickly find the resolve to make tough decisions in high-stress situations while keeping his humanity intact.

On the first day of junior high school, Mato Kuroi happens to run into Yomi Takanashi, a shy, withdrawn girl whom she immediately takes an interest in. Mato tries her best to make conversation with Yomi, wanting to befriend her. At first, she is avoided, but the ice breaks when Yomi happens to notice a decorative blue bird attached to Mato's phone, which is from the book Li'l Birds At Play. Discovering they have a common interest, the two form a strong friendship. In an alternate universe, the young girls exist as parallel beings, Mato as Black★Rock Shooter, and Yomi as Dead Master. Somehow, what happens in one world seems to have an effect on the other, and unaware of this fact, the girls unknowingly become entangled by the threads of fate.

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.

Modern Germany is plagued by an outbreak of Amalgams. Existing solely to wreak havoc, these cybernetic entities spawn from rotting flesh and can fuse with technology to gain new abilities. With society left in the wake of their destruction, the Xenogenesis Assault Team (XAT) is formed to suppress the threat. Alongside its primary mission to protect against the Amalgam attacks, the organization is also researching the newly discovered amalgamated humans which possess rational thought and are far deadlier than their non-sentient counterparts. Joseph Jobson is one such amalgamated human who has full control over his powers. Although successful in his line of work as a lone warrior, an unfortunate encounter with the recently-turned-Amalgam Gerd Frentzen makes him a priority target of the XAT. As he eludes the organization and seeks new allies, Joseph is transformed into the Blassreiter—a being heralded as the strongest Amalgam in existence. Now, he must fight back with his newfound powers to uncover the truth behind not only his past, but also the entire Amalgam conflict.