Ten years after the death of Light Yagami, the world believes the reign of Kira is over. However, Japan remains haunted by the power of the Death Note. The Tokyo Metropolitan Police Department maintains a diminished Death Note Countermeasure Task Force, but it has become a relic of a bygone era, lacking resources and respect. This is the setting for a three-part miniseries that bridges the gap between the original films and the 2016 movie Death Note: Light Up the New World. Each episode serves as a prequel, exploring the origins of the three main characters who will confront a new Kira outbreak.

The story unfolds across three interconnected chapters. The first chapter introduces Tsukuru Mishima, a brilliant but obsessive investigator often called a Death Note otaku. Recruited by the original task force, Mishima is a student of the Kira case, obsessing over the smallest details of Light Yagami's methods, including what brand of potato chips his allies ate. When a former criminal dies of a heart attack, Mishima investigates and uncovers a copycat killer using poison. However, the relief is short-lived. As he exposes the fraud, a real supernatural killer emerges, and a man believed to be a copycat suddenly dies of a heart attack while proclaiming the resurrection of Kira. This event triggers a new wave of mass heart attacks among criminals, proving a real Death Note is again in play and forcing Mishima to lead the hunt for a new god of the new world.

The second chapter shifts focus to Ryuzaki, the original successor to the legendary detective L. A famous international sleuth who has solved impossible cases from Hong Kong to Europe, Ryuzaki has repeatedly refused to involve himself with any Death Note investigation, honoring a promise he made to L. He is finally drawn into the case by a request from J, a woman connected to Wammy's House, to solve a bizarre locked-room murder. As he investigates, Ryuzaki uncovers the existence of two Death Note users: a cyber-terrorist and a mysterious woman. Forced to confront the reality that the Death Note has returned, Ryuzaki breaks his silence, revealing a flashback of his promise to L, and steps into the role his predecessor once held to battle the new Kira threat.

The final chapter explores the tragic past of Yuki Shien, the sole survivor of a brutal massacre that murdered his entire family. Traumatized and seeking a purpose, he becomes a cyber-terrorist operating in war zones, projecting his rage onto the world. He finds spiritual salvation in the legacy of the original Kira, whose judgment he believes freed him from his trauma. Shien becomes a radical Kira worshipper. His faith is rewarded when the Shinigami Ryuk appears, dropping a Death Note for him. Overjoyed, Shien begins his own purge, using his hacking skills to find another Death Note owner, Sakura Aoi. As he crosses paths with both Mishima and Ryuzaki, Shien embraces his role as a new apostle of judgment, setting the stage for the inevitable confrontation between those who would use the notebook for justice, for legacy, and for fanaticism.