The war between the Heike clan and the Genji clan continues. This time, Nozomi has to fight a powerful supernatural enemy and make a choice: protect her friends and stay by Kurou's side, or choose her first love, Masaomi, which is the leader of the Heike, and her enemy.

Rei Kigata is a first year middle schooler at Ishido Middle School. He is not a believer of any paranormal phenomena such as existence of ghosts or spirits in any kind, but one day at midnight, while he is sleeping, a mysterious newspaper called "Horror News" is delivered to his room. The newspaper tells a story in which one of his teachers at the school will get killed in a car accident the following morning and Kigata will be a witness of the accident. The story turns into a fact in the following day and since then, the mysterious newspaper is delivered everyday. He realizes he is haunted by this newspaper and that his life span would be shortened in 100 days every time he reads it. (Source: Crunchyroll, edited)

No longer concerned with military affairs, Yukichi Fukuzawa intends to act as a lone bodyguard-for-hire, making use of his deadly swordsmanship. However, things are not going as planned for his freelance business, and that is when he crosses paths with a mouthy boy named Ranpo Edogawa. While their initial interactions are intertwined with a bizarre murder mystery, the aftermath prompts the formation of the Armed Detective Agency. Presently, Ranpo finds himself chasing down a gifted individual with the dangerous ability to execute the perfect crime. But as the great detective unravels the case, he soon discovers an elaborate plot to obliterate the Agency in its entirety. Although forewarned of the trap, the Agency continue their pursuit of the criminals, only to end up framed for the crime themselves. Now branded as wanted terrorists, the remaining members must find a way to prove their innocence—even if they must turn to sworn enemies for assistance.

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.