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.

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.

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.

Aru deduces that the Eighth's diary is a server hosting and sending predictions to the blogs of her apprentices. When Yuki's diary predicts an attack by three of them, Aru has him moved to Kousaka's mansion. His plan is to lure the apprentices in, then deactivate the area's cell phone tower, severing their connection to the Eighth's server. Once the attack begins, however, Yuno appears and cuts the power to the tower remote control, wanting to defend Yuki by herself. Aru and Kousaka rush to deactivate the tower manually, while Yuki keeps Yuno in restraints. Two of Eighth's apprentices, Marco Ikusaba and Ai Mikami, manage to corner Yuki and Yuno by the time Aru deactivates the tower. However, Marco and Ai reveal that they are also the "owner" of a bona fide Future Diary, which has remained unaffected. With no other choice, Yuki releases Yuno, who intimidates the couple into retreating. When the third apprentice sets the mansion on fire, however, Marco and Ai counterattack. Their diaries' ability to predict each other's actions manages to overwhelm Yuno, resulting in her and Yuki getting injured and their diaries taken away. As Yuki and his friends are brooding in the hospital, they are approached by Uryu.

Aru deduces that Marco and Ai have not destroyed Yuki and Yuno's diaries because they want to take advantage of the information they provide. In order to confuse them, he has Uryu feed Yuki false information. Yuki's father visits him in the hospital, but while Yuki's away, he searches the room for his cell phone. Yuno overhears that he has promised to destroy it in return for the cancellation of his substantial debt and realises he is being used by the Eleventh diary holder. Marco, who's learned all about the situation from Yuki's diary, considers Yuki's father a useful link to Uryu and the Eleventh and calls Yuno, demanding that they bring Yuki's father to an abandoned commercial tower. Once they arrive, Marco places Yuki and Yuno's phones on a table and attacks Yuki's father. As Yuki futilely fights Marco, his father goes over to the table and breaks his phone. However, nothing happens. Yuno, who's realised that the phones were decoys, attacks Ai and successfully retrieves both diaries. Just then, Marco and Ai's apprentice friend sets off explosives. The floor under Yuki collapses and both his father and Yuno reach out to grab him. Meanwhile, Nishijima has uncovered the identity of Eighth, a children's caretaker called Kamado Ueshita, and goes to search her orphanage.

In a flashback, Marco and Ai are abandoned children who meet in the commercial tower, grow up in Kamado's orphanage and eventually fall in love. Yuki chooses to take Yuno's hand, while Marco and Ai run to the crumbling tower's roof with Yuki's father, intending to jump off with parachutes. Yuno catches up to them and once again tries to fight them alone, while Yuki hides and attempts to help her with his diary's predictions. Yuno loses and has her phone taken away, but it turns out to be Marco and Ai's decoy, which distracts them with false predictions. As a result, Yuno manages to critically injure Ai. Yuki's father grabs one of the two parachutes and escapes the tower, but he runs into Yuki's mother, who has been informed of the situation by Nishijima. When she threatens to turn him in, he stabs her. Yuki, Yuno and a dying Ai are trapped in the wreckage, but Marco attempts to free Ai despite having been mortally wounded himself. With Yuki and Yuno's help, the debris is cleared out and Marco and Ai die together as the tower collapses. Yuki and Yuno escape using the second parachute, only to find Yuki's mother has died. Meanwhile, Nishijima has been unable to find Kamado's Future Diary server.

Yuno expresses her disgust at how this state of affairs prevents her and Yuki from ever surviving together. She states that since Yuki won't kill her, she will kill him and travel back in time again to meet another Yuki. Murmur shoves Yuki off a cliff, but he is saved by the sudden reappearance of Uryu, who displays powers similar to Murmur's. Cornered, Murmur and Yuno travel two years back in time to a "third world", followed by Uryu and Yuki. Uryu explains to Yuki that when Deus realised Murmur was favouring Yuno, he suspected them of being from another timeline. In order to ensure the fair running of the game, he imparted Uryu with part of his power, although she did not know so at the time. Knowing that Yuno intends to kill her past self in this world as well, Yuki rushes to her house with Uryu. When Yuki finds the third Yuno locked in a cage and choking on a mat she tried to eat, he calls for an ambulance, despite Uryu's warnings about interfering with the past. Yuno and Murmur arrive with the third world's Yuki's parents and Uryu, Yuki and the third Yuno flee.

An ambulance arrives at Yuno's house together with the third Yuno's father. Although he is a much more caring man in this world, Yuno has to stab him when he starts getting suspicious of her. Uryu drops off Yuki and the third Yuno at the school and makes a phone call to this world's Keigo, forewarning him about his son's illness. Yuki evades Yuno and Murmur's attacks, trying to convince Yuno to return to the second world and rule as its goddess. However, Yuno, torn between her feelings for Yuki and the inevitability of the second world's destruction unless one of them dies, decides to trap him in an illusionary "ideal" world where his parents are alive and she has never existed. Uryu returns and fights Murmur, but she is overwhelmed once Yuno releases the seal on Murmur's powers. With Uryu beaten, Yuno approaches her other self.

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.