Ten years after the final confrontation between Light Yagami and L, the world has changed. Cyber-terrorism is rampant, and a new wave of inexplicable mass murders suggests that Death Notes have returned. The Shinigami King, intrigued by the chaos Kira created, has ordered six Death Notes to be sent to the human world, the maximum number that can be active at one time. This sets off a global race to secure the notebooks.

In Japan, a newly formed Death Note Task Force is led by the earnest investigator Tsukuru Mishima. He is reluctantly partnered with Ryuzaki, a brilliant but eccentric world-renowned detective who claims to be L's true successor. Their initial investigation begins in Shibuya, where they intercept a young woman named Sakura Aoi during a random killing spree. After she is killed, the Task Force claims her notebook and meets its Shinigami, Bepo, who confirms the existence of the six notebooks.

Complicating the investigation is Yuki Shien, a charismatic and ruthless cyber-terrorist who worships Kira. Using his hacking skills, Shien spreads a virus that broadcasts a pre-recorded message from the deceased Light Yagami, inciting global panic. He is on his own quest to collect all six Death Notes, believing himself to be carrying out Light's will. Shien tracks down Misa Amane, Light's former lover who has no memory of the Death Note after relinquishing ownership years ago. By giving her a notebook and restoring her memories, Shien attempts to learn the location of a "Promised Land" Light spoke of, but Misa refuses to cooperate.

A three-way battle ensues among Mishima, Ryuzaki, and Shien. Ryuzaki uses a digital recreation of L to lure Shien into a trap, but Shien anticipates the move and retaliates by killing Task Force veteran Touta Matsuda. The ensuing political fallout leads to the Task Force being disbanded. Undeterred, Mishima decodes a hidden message from Ryuzaki and discovers the detective is in possession of the final Death Note. When Mishima confronts him, Ryuzaki reveals his notebook is completely blank; he promised L he would never use it, and instead maintains ownership simply to see his attached Shinigami, a white female entity named Arma.

The investigation takes a personal turn when Mishima is arrested for his past failure to locate Teru Mikami, a prosecutor who was secretly guarding Light Yagami's son. Ryuzaki breaks Mishima out of custody, and they devise a final plan to lure out Shien. At a public square, the confrontation erupts. Misa, having now made the Shinigami Eye deal to regain her memories permanently, appears and seemingly kills Ryuzaki by writing his name. After revealing to Shien that Light is truly dead, a heartbroken Misa writes her own name in the Death Note, killing herself to join Light.

Shien proceeds to the "Promised Land," an abandoned hotel, only to be confronted by a very-much-alive Ryuzaki and Mishima. Ryuzaki reveals that his name was written in another Death Note days prior, with a delayed time of death, making Misa's attempt无效. He then deduces that Mishima is the true mastermind, the "Neo Kira." Forced to touch a Death Note, Mishima's erased memories return. He had witnessed Mikami kill Light's son in madness, and after shooting Mikami, Mishima succumbed to the power of the notebook and took the title of Kira for himself. To avoid suspicion, he gave up ownership and used Shien as an unwitting pawn to gather the other notebooks, all while already having written Ryuzaki's name with a future death date.

As the revelation unfolds, police special forces storm the building. Shien is killed in the gunfire, but Mishima and Ryuzaki escape. They are cornered by Task Force member Sho Nanase, who seeks revenge for her brother killed by the original Kira. As she prepares to shoot Mishima, Arma sacrifices herself by writing Nanase's name in her own Death Note, killing the officer but turning Arma to dust.

In the aftermath, Mishima is taken into custody. Ryuzaki, now fated to die on the date Mishima wrote, visits him in his cell. He reveals that four of the six secured Death Notes were destroyed in a terrorist attack, meaning the chaos will continue. On his final day, Ryuzaki trades places with Mishima, freeing him and bestowing upon him the mission to retrieve the remaining notebooks. As the new Ryuzaki walks free, the original Ryuzaki dies peacefully of a heart attack, while a post-credits scene shows a video file of Light Yagami smiling as he says, "Just as I planned."