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.

Losing a loved one is so painful that one may sometimes wish to be able to resurrect them—a weakness that the enigmatic Millennium Earl exploits. To make his mechanical weapons known as "Akuma," he uses the souls of the dead that are called back. Once a soul is placed in an Akuma, it is trapped forever, and the only way to save them is to exorcise them from their vessel using the Anti-Akuma weapon, "Innocence." After spending three years as the disciple of General Cross, Allen Walker is sent to the Black Order—an organization comprised of those willing to fight Akuma and the Millennium Earl—to become an official Exorcist. With an arm as his Innocence and a cursed eye that can see the suffering souls within an Akuma, it's up to Allen and his fellow Exorcists to stop the Millennium Earl's ultimate plot: one that can lead to the destruction of the world. [Written by MAL Rewrite]

Extra bits meant to add to the Blue Seed story. Episodes 1-13 are extras shown on the video releases of Blue Seed in Japan. They take place after every other episode, such as Omake 1 follows episode 2. Episode 14 is an extra featured with OVA Blue Seed 1.5.

Despite the recent Akuma attack, the members of the Black Order are in high spirits as they set about moving to a new base. Immediately upon his arrival, however, Allen Walker is suddenly called by the Central Agency and has his arm forcefully sealed by the Order. He is then led to a surprising meeting with his master, General Cross Marian, who reveals staggering secrets surrounding the enigmatic 14th Noah. A phantom thief incident, the arrival of a mysterious group of Exorcists, the death of an important comrade, and an all-out battle against the Noah Family—just what does this mean for Allen, Yuu Kanda, and the rest of the Order? This is but the beginning of a series of strange, seemingly unconnected events that lead to something far greater. [Written by MAL Rewrite]