Izumi Sakuragi is a new police sergeant with the Special Investigations Office, which was set up within the Metropolitan Police in November last year. The new investigation team uses DNA analysis and the latest in forensics science to investigate cold cases as well as cases suspected to involve missing persons.

Sakazaki Iwane is a ronin who spends idle days in Edo. Until a few months ago, he was a promising son and successor to a powerful family in Bungo. He has came back to Edo, where he lived for a while for swordplay training with his two best friends, after a tragedy in the three's home domain—both of the two friends died, one of them killed by Iwane by command of the domain lord's chief retainer. Iwane left his home for Edo, leaving behind his fiancée, a sister of the friend he killed. Eventually, Iwane detects the conspiracy behind the deaths of the two friends and struggles to reform his domain.

Koji carries an emotional wound from a missing childhood friend Sayoko, who disappeared when they were junior high school students. He left his hometown to forget about her and now, five years later, he goes to a grad school in Tokyo. One day, he gets a phone call from a former classmate and hears about the death of Sayoko's father. To attend his funeral, Koji returns to his hometown...