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.

In a flashback, Keigo forms an alliance with Uryu, promising to stop pursuing her and asking her to take care of his terminally ill son if he is eliminated from the Survival Game. Yuki and Yuno get arrested and brought to Keigo. In the interrogation room, Keigo forces Yuki to play a rigged game of Russian Roulette with his service revolver. Alerted to Keigo's treachery by her diary, Yuno knocks out the detectives guarding her and steals their guns. Just before Yuki gets shot, Yuno breaks into the room, injures Keigo and leaves with Yuki. Panicking, Yuki shoots at one of the policemen pursuing them. Since both Yuki and Yuno have now committed a crime, their actions can be detected by Keigo's diary, which was his plan all along. Trapped at the police station's roof, Yuki and Yuno jump off, but a truck's tarp breaks their fall. The next day, Yuki and Yuno are hiding from the police when they notice Keigo's wife visiting a hospital. When they follow her, they get ambushed by Uryu, who blows part of the floor up. After Yuki accidentally causes more of the floor to collapse, Uryu allies with Yuki in order to have Yuno pull them both to safety, incurring Keigo's wrath in the process. With their deaths foretold in all three diaries, Uryu takes Yuki and Yuno to the room where Keigo's son and wife are.

While the police surrounds the hospital, Uryu takes Keigo's wife and son hostage and tries to bargain with him. However, Keigo is convinced the only way to save his family is to win the survival game and refuses to negotiate. Yuki gets captured by the police, but as Keigo takes hold of him, Yuno appears, holding a grenade. Even when Keigo agrees to let Yuki go, Yuno decides to detonate the grenade, reasoning she'd rather die taking out Keigo than not be with Yuki. The grenade turns out to be a flash bang, knocking everyone out. Meanwhile, Uryu tries to escape the hospital, only to run into Nishijima. She tells him about the deal she and Keigo made and how he framed Yuki and Yuno, and they both rush back to the hospital. Yuki regains consciousness and tries to shoot at Keigo, but he uses Yuno as a shield. Despite his diary predicting he will kill Yuno if he shoots, Yuki refuses to give up, proclaiming his love for her. The future somehow changes and Yuki gets a clean shot at Keigo. Uryu arrives with Nishijima, who places Keigo under arrest. Since he's no longer a detective, his Investigation diary stops predicting the future. After learning his family has been rescued, Keigo asks Uryu to take care of his son, apologises to Yuki and breaks his own diary, removing himself from existence. Yuki and Yuno are exonerated thanks to files Keigo left behind, while Uryu escapes yet again. A few days later, Aru sends Yuki a text message warning him about Yuno, but she intercepts and deletes it.

When Deus realises that his assistant, Murmur, manipulated events to hasten Keigo's elimination, she claims she wants the game concluded before he has to "retire" and challenges him to a wager on the winner of the survival game, with her picking Yuno and Deus betting on Yuki. Yuki and Yuno go on a stargazing trip, but Yuno alters their destination along the way. Worried about Yuki's safety, Aru contacts Nishijima and they manage to narrow Yuki and Yuno's location down to a run-down holiday resort, enlisting Hinata, Mao and Kousaka to search for them. As they split up and search the abandoned hotels, Aru and Kousaka face various traps set by Yuno, while Hinata is tricked by a text message Yuno sent from Yuki's phone. When the others attempt to find Hinata, they get locked in a room which starts to fill up with gas. At the end of the episode, Yuki is shown bound to a chair, with an ecstatic Yuno sitting between two skulls.

Aru talks to Yuno through her surveillance feed, revealing he dug up three corpses from her garden, two of which had recently had their skulls removed. When he threatens to give this information to the police unless she releases them, the stress causes Yuno to alter her memory again, rendering negotiations moot. As Kousaka uses his cell phone to post his will in his blog, it is apparently turned into a Future Diary by the Eighth diary holder, who adresses him as an "apprentice". On Aru's advice, Kousaka acts out his diary's predictions, reaching an amnesiac Yuno, a catatonic Yuki and a bound Hinata in the control room. His appearance causes Yuki to recover, recalling how Yuno abducted him to keep him safe until July 28th. Yuno places the key to Yuki's shackles on the floor and tosses Kousaka the control panel key, allowing him to free Aru and Mao. Yuno then takes advantage of Kousaka's distraction and shoots at him with a crossbow. However, Yuki, having had his key kicked over to him by Hinata, frees himself and stops Yuno, leaving her behind when his diary predicts the imminent arrival of three diary holders, all apprentices of the Eighth.

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.

In a flashback, Yuno is revealed to have murdered her parents, who used to discipline her harshly for failing to meet their standards. After she fell in love with Yuki, he became her sole reason to live. Yuki asks Deus to bring his mother back to life, but he reveals that he is dying and his powers have faded. Furthermore, unless a successor is determined soon, all existence will collapse. When Yuki's father returns home, Yuki, who knows he killed his mother from his diary, demands that he turn himself in. However, his father points out that he has no evidence. The next day, Yuki goes after his father, expecting him to lead him to evidence. However, it turns out that Yuki's father wanted to visit the site where his family was going to go stargazing before he turned himself in. As Yuki reconciles with his father, they are ambushed by agents of Eleventh and Yuki's father is murdered. Enraged, Yuki fights back and manages, with Yuno's help, to kill the attackers. Afterwards, Yuki declares that he is now determined to win the survival game in order to attain the power to resurrect his parents. When he tells Yuno this means he has to kill her, she calmly replies that she is ready to die for him at any time.

The mayor of the city, John Balks, passes a motion to have Kamado's orphanage shut down. He then attends Deus' meeting, where Yuki and Yuno, having deduced his identity, expose him as the Eleventh diary holder. Uryu relays these news to Nishijima, who reveals he's been reassigned as Balks' bodyguard. Furthermore, he's discovered that Yuno was adopted. Yuno theorises that Balks wants to seize Kamado's Future Diary server, so she has Yuki form an alliance with her. Yuki, Yuno, Kamado and her apprentices ambush Balks' car on a country road, but he uses a jammer to sever connections to Kamado's server. Yuki and Yuno, who anticipated this, betray Kamado and slaughter her defenseless apprentices. Kamado flees in Balks' car, while Yuki and Yuno give chase. As Yuki and Yuno corner Balks and Kamado, Uryu appears with Aru. Aru reveals he's retrieved Yuno's umbilical cord from her orphanage and that its DNA matches the third corpse's, meaning that the real Yuno Gasai is dead and the one Yuki has known all along is actually an imposter.

Despite Aru's revelation, Yuki declares his trust in Yuno. Balks connects Kamado's server to HOLON, a supercomputer which holds user accounts of every citizen of the city, making them his apprentices. Uryu tries to attack Balks, but his diary lets him turn the tables. Nishijima, who's fallen in love with Uryu, comes to her aid and destroys the supercomputer. However, it turns out to be only one part of the whole, and Balks' plan is put into motion. As Aru sends Hinata, Mao and Kousaka to help Uryu and Nishijima destroy the remaining parts of HOLON, Uryu figures out Balks' diary can read the predictions of all other Future Diaries. Deus reveals to Uryu that Balks helped him design the Future Diaries, wishing to grant divine power to the human race. Uryu, Nishijima, Hinata, Mao and Kousaka storm HOLON's location, overwriting their diaries' predictions to confuse Balks. In response, Balks makes use of his secretary's diary and manages to capture Hinata, Mao and Kousaka, as well as injure Uryu and kill Nishijima. Uryu is saved by Yuki and Yuno, who've used her as bait to get to Balks.

Yuki and Yuno wreak havoc, demanding that Balks release their friends and commit suicide. Balks locks himself in a vault belonging to Yuno's parents' bank, which can only be unlocked by himself, Yuno's parents, and the real Yuno. Uryu, reasoning that Yuki can no longer eliminate Balks for her, starts hunting him. As she does, she tells him how she lost her parents in the Middle East as a child and grew up under the constant threat of death. At the same time, Yuno frees Yuki's friends and goes to kill Kamado, but she is stopped by Aru. In a tense showdown between Uryu and Yuki, the former sees her innocent child self in the latter and lets him shoot her. Uryu then destroys her diary voluntarily in order to detonate a bomb triggered by her death, intending to destroy the vault door for Yuki. However, the door withstands the blast. Yuno arrives, sends Yuki away to destroy HOLON, and somehow manages to open the vault door and kill Balks. A few days later, dark vortices appear all over the city. In Deus' realm, Murmur is panicking over the world ending sooner than expected, when Kamado appears with Aru, who asks Deus if it is really possible for his successor to return the world to the way it was.

Shocked at Deus' answer, Aru attempts to tell Yuki, but Deus stops him. Deus reveals that Aru is an entity created by him to observe and record information on the survival game and starts disassembling him, promising to spare him if he proves he has done anything out of his own free will. Aru succeeds when he reveals he had Kamado make his diary into an apprentice diary, wishing to change the future and save Yuki. As Yuki and Yuno arrive at Aru's apartment to kill Kamado, they're held off by Aru. Yuno starts fighting Aru, while Yuki chases after Kamado and his friends. When he runs into Hinata, she tells him what Aru learned from Deus: even the divine power bestowed to the winner of the survival game cannot bring the souls of the dead back. Meanwhile, Yuno, who has been cornered by Akise, stabs herself and calls Yuki, tricking him into thinking everyone is deceiving him. Yuki kills Hinata, Mao and Kousaka, believing he can bring them back to life later. Aru reaches Yuki and warns him that Yuno plans to kill him. Yuno catches up to Aru and they fight again. Although Aru breaks Yuno's diary, she doesn't vanish; she produces a second cell phone from her pocket, claiming the first one was a fake, and slashes at Aru's throat. As Yuno kills Kamado, a dying Aru, who knows the diary he destroyed was real, suddenly has an epiphany about Yuno. Since he can no longer talk, he writes a message in his phone and shows it to Yuki, allowing Yuno to finish him off as Deus collapses.

With a small core being all that remains from Deus, Murmur proclaims herself his successor until his death and the end of the world on July 28th. Yuno reminds Yuki about her diary's prediction that they will "become one" on that day. As the days pass, Yuki eventually admits to himself that his friends were probably telling the truth. Since he can't understand why Yuno would lie to him, he decides to get the truth from her by fulfilling her diary's prediction earlier. On July 27th, Yuki and Yuno make love, "becoming one". Afterward, Yuki asks Yuno why she lied about resurrecting people being possible. Yuno says that she just wanted to console him and asks him to kill her. Yuki refuses and instead suggests that they die together. When he mentions Aru's message, which claimed that this universe is a second iteration of a world in which Yuno became a goddess and travelled back in time, Yuno attacks him. As he runs away, Yuki is intercepted by Murmur, who shows him visions of the past. Murmur confirms that Yuno has indeed played the survival game once before. In the "first world", where she and Yuki also ended up as the last contestants, both agreed to commit suicide rather than having to kill the other. However, Yuno only pretended to kill herself, thinking she could bring Yuki back as a goddess. When she discovered she could not restore souls, Yuno, wishing to see Yuki again, travelled back in time and killed her other self, taking her place. Distraught at the death of the second Yuno, Yuki breaks out of the vision and confronts Yuno.

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.