The Chosen Children have been reunited with their Digimon partners, who no longer remember them due to the effects of a digital reset. While everyone tries to reconnect with their digital monsters, Sora Takenouchi encounters resistance from Piyomon, who stubbornly refuses to speak to her. Suddenly, an attack by a hostile Digimon separates the group, scattering them and their Digimon across the Digital World.

Back in the human world, Daigo Nishijima of the Incorporated Administrative Agency receives a warning that a new entity is in pursuit of "Libra," which he believes to be an alias for Meicoomon. For some reason, Meicoomon retains all of her memories and therefore still recalls her partner Meiko Mochizuki, who has come alone to the Digital World to find her. If they hope to identify what other forces have been driving the incidents thus far, the Chosen Children must survive the obstacles of the recreated Digital World and make their way back home.

[Written by MAL Rewrite]

The story begins when high school student Kazuki Muto is killed one night saving a mysterious girl from a monster, only to wake up in his school dorm, believing it to have been a dream; however, he soon finds out that dream wasn't a dream at all when a giant serpentine monster attacks him and his sister. Tokiko Tsumura, the girl he saved, explains that the monster is a homunculus. Kazuki had been attacked and killed by it when he was rescuing her; however, she, feeling responsible for him, revived him by placing a Kakugane medallion in his chest, serving as a replacement heart. The Kakugane, as Tokiko explains, is an alchemical device that, when activated, takes a certain form based on the Kakugane's user, forming a unique Buso Renkin. The Buso Renkin is the only thing that can destroy a homunculus monster. Using this, Kazuki creates his own Buso Renkin (the "Sunlight Heart," a huge lance). Along with Tokiko and her own Buso Renkin (the "Valkyrie Skirt," an execution scythe), Kazuki joins the fight against the homunculi and their master.

Deunan, a young female warrior, and Briareos, a veteran cyborg-soldier, are both partners and lovers. As members of E.S.W.A.T., the elite special forces serving Olympus, they are deployed whenever trouble strikes. The two fighters find their partnership tested in a new way by the arrival of a new member to their ranks—an experimental Bioroid named Tereus.

After obtaining the Number One headband, which proclaims him to be the best of all warriors, Afro spends most of his days in peace, though his nightmare-filled nights are not so tranquil. His life crescendos into chaos once again when Jinno and Sio, his former friends from long ago, take the headband from him, as well as the remains of his father. Challenged by Sio to don the Number Two headband again and exact revenge on them for their actions, Afro embarks on another journey as the wearer of said headband—an item for which anyone would kill him.

Afro Samurai: Resurrection follows Afro as he fights a second series of battles against all manner of foes, wading through the sea of corpses in his wake so that he may once again quench his never-ending thirst for revenge.

[Written by MAL Rewrite]