This movie introduced Rem, the Shinigami who gave a second Death Note to Misa. Misa used her Death Note to attempt to make contact with Kira (Light) and made the Shinigami Eye trade. Using this power she discovered that Light was Kira, and tracked him down.
When she found him, she declared her devotion to him and gave him her Death Note as proof, and in exchange, he agreed to go out with her. Soon afterward, Light encountered L on the university campus, wearing a mask so that his face could not be seen. Misa turned up to say hello to Light, and Light manipulated the circumstance so that Misa could see L's face, and therefore his name. However, L had already deduced that Misa was the Second Kira, and he had her captured and imprisoned before she could tell Light his name.
Misa gave up her ownership of the Death Note and lost all memory pertaining to it, and thus once captured she honestly remembered nothing about the Death Note, the Shinigami, or being the Second Kira. Light then used the same trick, burying his own Death Note in the forest for future retrieval, and allowed L to capture him and lock him up, telling Rem to give Misa's Death Note to someone else.
After several days, the Kira deaths stopped, but then resumed when the new owner of Misa's Death Note began to use it. L authorized Misa's and Light's releases, but Misa was required to stay in a secure, though comfortable, compound. L and Light hunted down the new owner of the Death Note, Kiyomi Takada, and captured her and her Death Note, then coming to see Rem.
However, upon touching the Death Note, Light remembered everything that had happened before. The case was "solved", and Misa released, but Light made her touch a piece of her previous Death Note so that she would regain her memories. Light said goodbye to her, and asked her to dig up his previous Death Note and write L's name in it. Meanwhile, Light remained in the compound with L, and Soichiro took possession of the Death Note obtained from Kiyomi, leaving it in a secure suitcase. The team went with him, leaving L and Light alone together.
Misa dug up the Death Note, 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 that he has decided that Misa is definitely one of the Kiras and must die.
Rem is furious that L has arranged Misa's demise, and writes both L's and Watari's names in her Death Note. Both of them fall to the floor soon afterward, 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 had obtained Misa's Death Note during her imprisonment, and had 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 this, he had written his own name on that Death Note, arranging to die peacefully at the very 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. It is also implied that the Death Note that Misa found in the forest was a fake.
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 anything. As a last-ditch attempt to eliminate his opposition, Light begged Ryuk to write their names in his Death Note. 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.