Set in 1988 in Hiroshima, Japan, prior to the enactment of the anti-organized crime law. A rumor exists that Detective Shogo Ogami has ties with the yakuza. He is partnered with Detective Shuichi Hioka and they investigate a missing person case involving a financial company employee. Conflicts between opposing yakuza groups become more serious.

Maebara Keiichi, a young teenager, has recently moved from the city to the rural village of Hinamizawa with his family. He is adjusting quite well to his new life, making friends at the small school, playing games, passing time in relative happiness, when suddenly a gruesome murder occurs. A mystery begins to unravel — tracing back to happenings five years ago. As Keiichi learns more about these strange events, he wonders if he will be able to face the truth behind all of this.