Yukiteru "Yuki" Amano is a loner who spends his time texting in his cellphone diary, playing darts and talking to his imaginary friend, Deus Ex Machina, the God of Time and Space. One morning, he finds his diary entry for the day filled in already, and the events recounted in the diary strangely start coming true. Yuki is then startled upon learning that Deus is an actual deity, who reveals to Yuki that his diary can now predict his future, but also warns him that he will die if his diary is destroyed. As Yuki starts using the diary to his advantage, he is approached and stalked by model student Yuno Gasai, who possesses the Second Future Diary, which foretold his death at the hands of his homeroom teacher Takao Hiyama, secretly a serial killer who owns the Third Future Diary. As Yuno helps Yuki evade Takao, Yuki is able to hit Takao's cellphone with a dart, causing Takao to vanish into a vortex. Afterwards, Deus summons a congress and explains the rules of the survival game to the remaining eleven Future Diary Holders, including Yuki and Yuno, in which they all must try to kill each other in order to win the right to succeed him. Deus's assistant, Murmur, introduces Takao to the survival game. However, when Murmur tries to give Takao a cellphone diary, he keeps destroying it, causing him to repeatedly vanish into a vortex.

Minene Uryū, a terrorist and the Ninth Future Diary Holder, holds the school hostage, having rigged its corridors with motion sensor bombs. As Yuki combines his ability to predict everything happening around him with Yuno's ability to predict everything happening to Yuki himself, the two manage to evade danger, until Minene threatens to detonate all the bombs unless Yuki is handed over to her. Yuki is captured by his classmates, angering Yuno, who runs down the corridors and causes several classrooms to explode on purpose. Yuki and Minene are soon confronted by police officer Keigo Kurusu, the Fourth Future Diary Holder who is able to predict crimes. Keigo, who is Minene's true target, reveals he is not interested in the survival game and just wants to stop criminals. Yuno, Keigo and all the classmates work together to distract Minene, allowing Yuki to throw a dart at her Future Diary cellphone. However, Minene dodges it, injuring her left eye and uses her ability to escape. In the aftermath, Keigo forms an alliance with Yuki and Yuno to stop the other Future Diary Holders. Murmur introduces herself while flowing down a river. She reviews that Keigo and Minene both found out about Yuki, since they both were after Takao, who Yuki killed already. Murmur says goodbye while drifting off a waterfall.

Keigo sends Yuki and Yuno to an amusement park to act as bait for Minene. When Yuki asks Yuno why she keeps following him around all day, she reminds him of when they first met one year earlier. Yuki was depressed over his parents' divorce, and Yuno offered to marry him in the future to cheer him up. Although Yuki realizes Yuno is still hiding something from him, she refuses to divulge anything more. That night, Yuno invites Yuki to stop by her house. While searching for the bathroom, he opens a bizarre door to a room containing three decomposed corpses, an act which changes the future of every Future Diary Holder drastically and causes a causality continuum breakdown, much to Deus's excitement. Terrified, Yuki runs home, only to find Yuno right outside his door. Meanwhile, Minene finds evading the police difficult, despite her ability to secure escape routes. Exhausted and cornered, she is approached by a mysterious man, who offers to save her and takes her to a hut in the woods. There, he reveals himself as a Future Diary Holder, drugging and torturing her to get information on other Future Diary Holders. Murmur, who wants to be more popular, asks for Yuki's advice, and he tells her that being a good cook might help. She prepares corn in different ways, them being boiled, roasted, streamed, fried and dried. Yuki says that being kind by making a midnight snack would be a better idea. Later, Deus appears surprised by a random dish of food that appears next to his throne.

In a flashback, Tsubaki became the priestess of the Omekata cult after her parents fooled people of her clairvoyance, but she was raped by the male followers after her parents died in a car accident and lost a ball that once belonged to her mother that helped maintained her sanity. In the present, as Yuki, Yuno, and Tsubaki flee, they are halted by Yomotsu with four hypnotized cult members dressed like him, who explain that he used the diary from his tape recorder to find Tsubaki, intending to kill her using an explosive device inside of him. Since Yomotsu is blind, Yuno manages to tell him apart from the others and kill him. After Tsubaki reveals to Yuki and Yuno that her plan all along was to kill them, Yuno cuts off Tsubaki's right hand and gives Yuki her cellphone, before collapsing from exhaustion and being captured. Yuki avoids them undetected using both diaries, but Tsubaki lures him out by announcing Yuno will be raped and killed by her followers. He manages to reach Yuno in time, but Tsubaki gloats that her scroll will predict his every action as long as he is in sight of her followers. Yuki throws Tsubaki's ball he found earlier up in the air, causing all of her followers to look at it. As her diary is rendered useless, Yuki throws a dart at her scroll and pierces it, causing her to vanish, and allowing Yuki and Yuno to escape. Meanwhile, Minene, who was released by Yomotsu, later gets captured by Keigo, who releases her in return for her contact information.

Knowing from her diary that Yuki's mother, Rea, is coming home from work abroad as a video game programmer, Yuno breaks into his house with the intention of introducing herself to Rea. Despite Yuki's efforts, Rea and Yuno meet, and take a liking to each other, sharing a good dinner and viewing Yuki's baby pictures, much to his embarrassment. Elsewhere, Minene gets her eye checked and catches sight of a few little children, especially one in particular. That night, Yuno reveals to Yuki that her diary predicts they will "become one" on July 28, and tells him she will do anything to make sure that future comes to pass. The next day, Rea brings home a young boy whose parents were killed at the Omekata cult incident, Reisuke Houjou, who, unbeknownst to everyone, is a Future Diary Holder.

Reisuke, the Fifth Future Diary Holder with a coloring book to predict in the day and night, makes several attempts to kill Yuki and Yuno, but the two of them thwart his attempts, soon realizing who he is. Yuki searches vigorously for Reisuke's diary in vain, while Yuno insists killing him would be faster. Yuno gives up and starts chasing Reisuke around the house with a hammer and accidentally hits Rea in the head and knocks her out. Yuno figures out that Reisuke has mailed his diary to himself in order to hide it and has Yuki intercept the delivery, but he falls prey to a nerve gas trap hidden in the envelope. Reisuke challenges Yuno to a hide-and-seek game inside the house filled with nerve gas, promising the antidote if she manages to capture him. Although Yuno evades numerous traps set by Reisuke, she finds herself at his mercy. However, Yuki intervenes, injuring Reisuke with a dart and giving Yuno the resolve and opportunity to finish him off. Yuki and Yuno collapse before managing to use the antidote, but Minene, who has been informed about the situation from Keigo, appears and saves them. As she walks away, she says that Yuki must kill Yuno, before she becomes an enemy.

Karyuudo Tsukishima, the Tenth Future Diary Holder, requests to transfer his diary's ownership when Deus calls a meeting for the eight surviving Future Diary Holders. Two weeks after Reisuke's disappearance, Yuki and Yuno transfer to a new school, while a group of serial killers are terrorizing the area. After school, Yuki and Yuno sneak in one of the crime scenes with Yuki's classmates, Ouji Kosaka, Hinata Hino, and Mao Nonosaka. When Hinata wanders off, Yuki's diary predicts her being attacked. Yuki rushes everyone to the scene, where they find Hinata's body before a pack of vicious dogs. A strange boy named Aru Akise appears and leads everyone to a nearby observation tower. Aru explains that he is one of Yuki's classmates and that he has been investigating the strange events in which Yuki keeps getting involved. Despite Yuno's mistrust in everyone, Yuki decides to reveal the existence of his diary in order to defend the group against the dogs. After they retreat, Mao takes Yuki's diary at knifepoint and hands it to Hinata, who is alive and well. After knowing Hinata is a Future Diary Holder, she reveals that her real target is Aru, suspecting him as a Future Diary Holder.

A week ago, Hinata received her diary, with the ability to control dogs on her command, from her dog breeder father Karyuudo, who wanted her to eliminate Aru. Back in the present day, Aru challenges Hinata to guess which hand he is hiding a coin in, with his diary as the forfeit. Despite using Yuki's diary, Hinata loses and has to release Yuki. However, Yuno realizes that Aru is not a Future Diary Holder, relying on bluff and observation instead. Aru proposes one more round of his game, with Yuki's diary on the line. He manages to guess correctly this time, seeing that Yuki's diary predicts what only Yuki perceives. Mao attempts to destroy Yuki's diary, but Yuno injures her. Yuki, Yuno, Aru, and Kosaka leave the park, while Hinata uses her diary to send the dog pack after them. Before Yuki decides to reason with Hinata, Yuno reaches her first and threatens to kill her. To pacify Yuno, Yuki forcefully becomes her boyfriend. Karyuudo communicates with everyone via radio, explaining that he mistook Aru as a Future Diary Holder, and after he warns Yuki about Keigo, who kills Karyuudo.

While making bombs for Keigo, Minene remembers the time when she was captured by a detective named Masumi Nishijima while confronting Takao. Although they developed a rapport as they evaded and defeated the killer, Minene ended up knocking Nishijima out to escape. Aru sets up Yuki and Yuno on a date to a bridal fair for a mock wedding, where they meet Keigo's wife, Naoko, while he investigates Yuno's house. When Yuki and Yuno return, they find Aru at the door of the room with the corpses. However, the wall is demolished and the corpses are buried in a deep hole in Yuno's garden. Even though this is Yuno's doing, she has no recollection of the event, and neither of Yuki visiting her house before. Aru theorizes that Yuno's mental balance is so fragile that she modified her own memories as a defense mechanism. Meanwhile, Keigo frames Yuki and Yuno for Karyuudo's death.