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.