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Misa dug up the Death Note, and regained her memories, but could not remember L's name, so she made the Shinigami Eye trade a second time, with Ryuk. She visited Light at the compound, determined to see L again and reveal his name a second time. When she arrives, L reveals to Light that he has decided that Misa is definitely one of the Kiras and will catch her in the act of writing his name in her Death Note.

Rem is furious that Light has arranged Misa's demise, and writes both L's and Watari's names in her Death Note. Both of them collapse to the floor soon afterward, supposedly dead. Rem, having used her Death Note to extend Misa's life, dies.

After L's death, Misa came down and met Light, giving him her Death Note again. Light wrote his father's name immediately, shocking Misa, and arranged that he should die after bringing Light his Death Note. True to what was written, Soichiro arrived with the suitcase, but opened it to reveal that it was empty, and he remained standing. Light was shocked.

As the rest of the investigation team converged on Light, L re-emerged, alive and well. He revealed that he'd had the Death Note Misa dug in the forest stolen and replaced with a fake. L discovered that deaths could be arranged up to 23 days in advance, as well as that anything written could not be changed. Three days prior to Rem writing his name, he had written his own name on the other Death Note, arranging to die peacefully at the maximum limit of that 23 days. Rem's writing of his name had had no effect because his name had already been written in a Death Note, though he lamented Watari's death.

Light, in frustration, attempted to use a piece of the Death Note hidden in a secret compartment of his watch, but Matsuda shot him before he could do so. As a last-ditch attempt to eliminate his opposition, Light tried persuading Ryuk to write their names in his Death Note (and extend Light's life). Ryuk, however, refused to do this, and instead wrote Light's name in his Death Note. Light pleaded, to no avail, and finally died in his father's arms while Misa watched in horror. L was given possession of all the Death Notes, but informed Ryuk, much to the Shinigami's dismay, that they would all be burned.

Afterward, Interpol closed the case. Twenty days later, after being congratulated by Soichiro, L died peacefully while eating his sweets, with a picture of Watari next to him.

One year after these events, the Yagami family visited Light's grave. Sayu reveals her belief that Light died in the fight against Kira, and Soichiro hoped only that Sayu would never find out what had really happened to Light. Somewhere else, Misa wondered about the gaps in her memory and felt that something was missing, but she did not know quite what. The movie ended with Ryuk flying past Tokyo Tower.