Yukiteru Amano is a loner who spends his time writing in his mobile diary and talking to an imaginary friend, Deus Ex Machina. However, one morning, he finds his diary entry for the day has been filled in already. Stranger yet, the events portrayed in the diary start coming true. Deus, who reveals he is an actual God, warns Yukiteru that if he loses his diary, he will die. As Yukiteru starts using the diary to his advantage, he is approached by a stalker named Yuno Gasai who also possesses a Future Diary that foretold his death at the hands of a serial killer, another Future Diary owner. Helping him evade the killer, Yuno helps Yukiteru throw a dart into the killer's phone, killing him. Afterwards, Deus explains the rules of the survival game to Yukiteru and the other diary owners, in which they must try to kill each other in order to win the right to succeed him.

Yomotsu appears before the fleeing Yuki, Yuno and Tsubaki with four hypnotised cult members dressed like him. Yomotsu explains that his Righteous Diary led him to infiltrate the Sacred Eye cult and that he intends to blow himself and Tsubaki up using Uryu's bomb. Having learned from Keigo that Yomotsu is blind, Yuno manages to find and kill him. Tsubaki then has her followers capture Yuki and Yuno, revealing her plan was to kill them, Keigo and Yomotsu all along. Due to her traumatic past as a ritual rape victim, Tsubaki wishes to attain Deus' power in order to remake the world. Yuno manages to kill the guards holding her, cut off Tsubaki's hand and hand Yuki her diary before collapsing from exhaustion. Using both diaries, Yuki manages to avoid detection, until Tsubaki tries to lure him out by announcing that her followers will rape and kill Yuno. Realising Yuno's devotion to him, Yuki gathers his courage and manages to reach Yuno on time, but Tsubaki gloats that as long as he's in sight of her followers, his actions will be predicted in her diary. Yuki throws a small ball he found earlier up in the air, causing all of Tsubaki's followers to look at it and rendering her diary useless. Yuki then throws a dart at Tsubaki's diary, and since she is missing a hand, she is unable to deflect the shot. With her diary pierced, Tsubaki vanishes and Yuki and Yuno escape. Meanwhile, Uryu, who was released by Yomotsu, gets captured by Keigo, but he eventually lets her go in return for her contact information.

After some hesitation at seeing the innocence of her other self, Yuno lunges at her, but she is stopped by her other self's parents. Meanwhile, the actions of Yuki and Uryu have caused a domino effect that has changed the future of almost every diary holder for the better. When Balks reads about his other self's death in Yuki's diary using his incomplete Watcher Diary, he calls off his partnership with Deus, who decides to cancel the survival game and find another method to determine his successor. Yuki manages to remember Yuno and break free from the illusionary world, in the process releasing his world's Murmur, who had been trapped by her first world self in order to impersonate her. Faced with Yuki's love and her other self's united family, Yuno's resolve to kill them all is lost, and she decides to commit suicide. A horrified Yuki is declared winner of the survival game by his world's Murmur and spirited away through a vortex. 10,000 years on, Yuki is still grieving Yuno's death in his now empty universe, refusing to create anything. At the end of the episode, the final entry in his diary changes from "Yuno died" to "Yuno came to see me", and her voice is heard calling his name.