After writing his own name in the Death Note to bring an end to the Kira case, the world’s greatest detective, known only as L, has just 23 days left to live. In the wake of solving that case and losing his loyal partner Watari, L uses his remaining time to take on the most urgent files Watari left behind, solving smaller crimes from his headquarters. A mysterious package addressed to Watari arrives containing a young, mute boy. The child is the sole survivor of a village in Thailand that was completely destroyed to contain an outbreak of a horrific artificial virus, a bio-weapon ten times more fatal than Ebola and highly contagious. The boy carries an SD card with data on the virus, making him a target for the eco-terrorist group that created it, a organization known as Blue Ship.

Soon after, a teenage girl named Maki Nikaido seeks out L. Her father, a scientist forced to work on the virus, injected himself with the pathogen and destroyed the only cure to prevent its use. Before dying, he sent Maki to L with crucial research data. Pursued by the terrorists, L takes both children under his protection. He is joined by a determined FBI agent named Suruga, who has his own mission to recover the Death Note. As L analyzes the data, he discovers the virus is a fusion of Ebola and influenza, engineered by a former Wammy’s House prodigy codenamed K. Her goal is to release the virus to dramatically reduce the human population and "save" the planet. To complicate matters, Maki reveals she has injected herself with the virus to keep a sample safe, turning her own body into a ticking time bomb.

The narrative focuses on L’s race against his own mortality and the virus’s activation. Traveling in secret, he works with a former colleague of Maki’s father to synthesize a new antidote. Throughout this journey, L is forced to move beyond his usual detached, intellectual methods, physically running, hiding, and forming an uncharacteristically paternal bond with the two children. The boy demonstrates extraordinary mathematical genius, leading L to eventually name him Near, a nod to his potential as a successor. The climax occurs when K kidnaps Maki and boards a commercial airplane, intending to use the infected girl to spread the virus globally. L arrives at the airport with the newly created antidote. He confronts K not with intellectual superiority, but with an appeal to her humanity, convincing her to abandon her plan. He saves the passengers by administering the cure. With his last day approaching, L leaves Near at the Wammy’s House orphanage to be trained as his successor. The story ends as L walks away from the world he helped save, quietly accepting his fate in the final hours of his life.