Yuki is trying to figure out the reason behind Yunos Future Love Diary when a woman named Uryuu Minene interrupts him. She quickly identifies him as the 1st and announces that she is the 9th and that the 1st will die.

Having escaped with their lives from the 9ths death trap at the school Yuki and Yuno find them selves in an alliance with the 4th diary holder Detective Keigo Kurusu. The 4th asks the two of them to spend the day together at an amusement park to act as bait for the 9th who continues to elude the 4th and his detective diary. At the end of the day Yuki uncovers an unsettling secret about Yuno and the 9th may have fallen into a trap set by someone other than the 4th.

Yuki is unable to tell anyone about the corpses he saw in Yuno's house, fearing she will find out through her diary. The next day, Keigo, Yuki and Yuno visit the Sacred Eye cult, where Uryu is being held prisoner. The cult's leader, Tsubaki Kasugano, is the holder of the Clairvoyance Diary, a scroll which tells the future as seen by her followers and has foretold her death by the end of the day. Since Yuki has already evaded death twice, Tsubaki asks that he stay with her for the night in exchange for handing over Uryu, which he accepts, much to Yuno's resentment. At night, Tsubaki's followers fall under the mind control of Yomotsu Hirasaka, the diary holder who captured Uryu, and close in on Yuki, Yuno and Tsubaki. Yuno starts hacking at the followers with an axe and poses an ultimatum to Yuki: join her or die.

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.

Knowing from her diary that Yuki's mother is coming home from abroad, Yuno breaks into Yuki's house with the intention of introducing herself to Yuki's mother. Despite Yuki's efforts, his mother and Yuno meet and take a liking to each other. That night, Yuno reveals to Yuki that her diary predicts they will "come together" on a certain date and tells him she will do anything to make sure that future comes to pass. The next day, Yuki's mother brings home Reisuke Houjou, a young boy whose parents were killed at the Sacred Eye incident. Despite his young age and precocious demeanor, Reisuke is a Future Diary owner, plotting Yuno's death.

Reisuke tries several times to kill Yuki and Yuno, but the two of them thwart his attempts, soon realizing he is a diary owner. Yuki starts searching for Reisuke's diary in vain, while Yuno insists killing him would be faster. While chasing Reisuke with a hammer, Yuno ends up injuring Yuki's mother instead. Yuno figures out that Reisuke has posted his diary to himself in order to hide it and has Yuki intercept the delivery, but he falls prey to a poison gas trap hidden in the envelope. Reisuke challenges Yuno to a hide-and-seek game inside the poison gas filled house, promising the antidote if she manages to capture him. Yuno evades numerous traps set by Reisuke, but eventually finds herself at his mercy. However, Yuki intervenes, injuring Reisuke with a dart and giving Yuno the resolve and opportunity to finish him off. Yuno and Yuki collapse before managing to use the antidote, but Uryu, who has been informed about the situation from Keigo, appears and saves them. Before leaving, Uryu tells Yuki not to trust Yuno.

Deus calls a meeting of the eight surviving diary holders, one of whom requests to transfer his diary's ownership. Two weeks after Reisuke's disappearance, Yuki and Yuno transfer to a new school, while a series of brutal murders has been terrorizing the area. After school, Yuki and Yuno sneak in one of the crime scenes with Yuki's classmates Hinata, Mao and Kousaka. 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 called Aru Akise appears and leads everyone to a nearby building. Aru explains that he's 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 pack's attacks. After the dogs suddenly retreat, Mao takes Yuki's diary at knifepoint and hands it to Hinata, who is alive and well. Hinata reveals she is the holder of the Breeder Diary and that her real target is Aru, whom she reveals as another diary owner.

In a flashback, Hinata receives the Breeder Diary from her dog breeder father, who wants her to eliminate Aru. When Hinata demands Aru's diary, he challenges her to guess which hand he's hiding a coin in, with his diary as the forfeit. Despite using Yuki's diary, Hinata loses and has to release Yuki. Yuno, however, realizes that Aru is not a Future Diary owner, relying on bluff and observation instead. Unfazed, Aru proposes one more round of his game, with Yuki's diary on the line. By intending to tell Yuki that he lost, no matter what the outcome, Aru manages to neutralize Yuki's diary, since its predictions are based on Yuki's perception. With the game thus reduced to a 50/50 gamble, Aru manages to guess correctly. Mao attempts to destroy Yuki's diary, but Yuno injures her. Yuki, Yuno, Aru and Kousaka leave the park, while Hinata uses her diary to send the dog pack after them. Yuki decides to return to Hinata and try to reason with her, but Yuno reaches her first and threatens to kill her, as well as anyone who attempts to come between her and Yuki. To pacify Yuno, Yuki is forced to declare her his girlfriend. Hinata's father communicates with everyone via radio, explaining that he mistook Aru for a diary owner and warning Yuki about Keigo before being killed by him.

While making bombs for Keigo, Uryu remembers the time she was captured by a detective called Nishijima while confronting the serial killer diary holder. Although they develop a rapport as they evade and defeat the killer, Uryu ends up knocking Nishijima out to escape. Aru sets up Yuki and Yuno on a date to a bridal fair, where they meet Keigo's wife, 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 has been demolished and the corpses buried in a deep hole in Yuno's garden. Even though this is Yuno's doing, she has no recollection of the event, nor of Yuki visiting her house before. Aru theorises that Yuno's mental balance is so fragile that she modified her own memories as a defense mechanism. Meanwhile, Keigo frames Yuki and Yuno as suspects for his murder of Hinata's father.