Initialization (初期化, Shokika) is the thirteenth and final episode of Season 2 of the Future Diary anime and is overall the series finale.
Muru Muru, who returned to normal, contemplates her victory over Second World Minene and heals Yuno's father to avoid a paradox. With everything set, Muru Muru tells Yuno to kill her third self. Yuno thinks that after killing her third self, everything will be fine so as long as she says goodbye to the second Yuki and meets the third one. Her third self slowly awakens as she calls her parents, and asks the First World Yuno who is she. First World Yuno does not reveal her identity but tells her third self of the horrible events that she will eventually go through. However, her third self says she's not suffering. Angered, Yuno says that what she says is a lie, that she's in fact suffering, but the third Yuno insists she is not suffering as she has faith her family can be loving once more if she endures it, as she loves her parents. Yuno remembers in shock that what her third self says is true and that she indeed believed her suffering would end, as she begins to wonder how did she become what she is now. First World Yuno states that she has somebody to see, and her third self asks if she has somebody she loves.
Muru Muru contemplates in horror that the Causality Continuum is being altered drastically and the source comes from within the illusionary world. Within the fantasy, Yuki begins to behave strangely and his father asks what's wrong. Yuki says he is sorry but that he cannot go see the stars as planned. His mother responds that he was so looking forward to stargazing with them. Yuki affirms that he does want to see the stars, but he has a feeling he needs to do something important.
Back in the third world, Keigo Kurusu arrives at Sakurami Middle School along with Masumi Nishijima and Saika Gasai. She sees her husband on the roof and leaves to go to him in a rush, prompting Kurusu to command Nishijima to check if there is anybody hurt. Muru Muru sees in shock that the Continuum is undergoing a massive changes, urging Yuno to quickly kill her third self. Meanwhile, Nishijima finds the hurt but still alive Second World Minene.
The future changes as a member of the Omekata Cult informs Tsubaki that there is a bomb in her parents' car, and the culprit is detained and shown to be Funatsu. He berates Tsubaki calling her a foolish girl who cannot do anything on her own, but Tsubaki reaffirms that the Cult exists to help the weak and is not for evil. Muru Muru notices the Third World Tsubaki's future has changed, and that with this change Reisuke's future has also changed as his parents no longer join a twisted sect. In a dark alley, vigilante Yomotsu apprehends the serial killer Hiyama. The murderer asks him if he's "the freak" that has been appearing lately, to which Yomotsu answers he's not a freak but a hero. In the Dog House owned by Karyuudo, he notices the dogs being quiet and finds his daughter Hinata attending to them. When Karyuudo asks Hinata about what she is doing, she replies that she is his daughter, and claims she has been with them for a rather long time, and asks her father if he could teach her how to train them. In the Mother's Home, Kamado receives a call from John Bacchus regarding assistance for the orphanage. Orin Miyashiro receives a call from Ai and says the orphanage is fine. Back in their apartment, Ai says to Marco that everything is fine, and Marco suggests they go to sleep as they have nothing to worry about now that they know the orphanage is safe. John is asked by his secretary if everything is okay, and John says it is as if the future is changing, and that his Diary, even though incomplete, has predicted his own death. John then goes to talk with Deus and says that his Diary has not only predicted his death but how Yuno will not save the world but instead time leap back to the past, which causes Deus to think of a new way to select his successor.
Muru Muru notices that the futures of all the Diary Holders have been altered and with such rapid changes, the Second World and the game are in danger. First World Yuno reads some entries in her own Diary that shows that she is still worried about Yuki who is trapped. She tells her third self that she wants to be with Yuki and that she must kill her for that to happen.
She attempts to kill her third self, but her father jumps in front to protect his daughter and takes her knife in his right shoulder. Yuki in the illusionary world says to his parents that he must do something even if he wants to go with them, and his parents ask him if it is about "the girl he cannot remember." Yuki's parents encourage him to go, saying that he is their son. Back in the Third World, Saika arrives and finds Ushio and the third Yuno, and rushes to their side. Yuno thinks of how she always believed that they could be a family again but that day never came. Third World Kurusu holds Yuno at gunpoint asking if she is the cause of the destruction, while Yuno realizes the future has changed because of Yuki's actions.
Meanwhile, Yuki's parents tell Yuki that he will be able to remember that girl's name as he prefers her over the fantasy and that he should do what he thinks is right. Yuno contemplates her actions and feels that what she is doing is not right, but in a fit of despair decides to kill the third Yuno and her parents and rushes to attack. However Yuki, who slowly calls out Yuno's name, finally remembers her name and says it, breaking the illusion. Yuno does not understand, but Yuki says that he is here to save her. Kurusu shoots at the attacking first Yuno, but the Muru Muru of the second world that was trapped with Yuki blocks the bullet from Kurusu, and she quickly restrains the Muru Muru of the first world in revenge.
First World Yuno happily embraces Yuki as she sees he has chosen her over his dreams, but Yuki asks her to kill him as she does not belong in the third world and he is ready to die to create a better place for her. Yuno reads her Diary and agrees to his wish. Muru Muru thinks that it is fine if Yuno wins the game. Yuki says that since he has killed a lot people he can accept death; however, Yuno stabs herself instead. When Yuki asks why, she responds that she cannot kill him and this is how the future should be. The dying Yuno's final request is one final kiss from Yuki, to which he complies. Her Diary reveals that even though she is dying she is at peace, and she praises Yuki's improved kissing.
As Yuno dies in Yuki's arms, the second Muru Muru, with the fragment of Deus in her hand, recognizes Yuki as the victor and forcibly takes him back to the second world to become its god.
In the third world, the second Minene has married Nishijima, and they have two children together. She watches the news reports that says her third self is in Japan. Minene jokingly praises her third self, and Nishijima says she should not say it as if it was not her concern, and Minene just says to Nishijima to do his best to "catch her again." Nishijima phones Kurusu and apologizes for not picking him up on time., Kurusu is seen with his wife and his son, who is alive and recovering.
Yomotsu pays a visit to Hiyama in prison, and the former serial murderer asks him if he does not have anything better to do.
Ai and Marco happily drinking tea outside a cafe. Marco apparently is having difficulties finding and keeping a job but the pregnant Ai lovingly encourages him.
Reisuke is seen happily enjoying his time with his loving parents.
Tsubaki's parents cover her with a blanket when they notice that she has fallen asleep which makes her smile.
Orin is seen with a fellow orphan, wishing a safe trip to both Kamado and John who appear engaged. Kosaka is seen with Akise and a female dog, being watched by Hinata and Mao who are wondering what are they doing, before Karyuudo says it is time to leave, to which they all happily comply. Deus asks Muru Muru what has the observer said, and she says there is no further interference from other dimensions.
The third Yuno is seen to live a happy and normal life hanging out with friends. Yuno reveals a new normal Diary with family pictures to her friends, but she mentions she feels as if she has forgotten something. As she says this she the third Yuki along with his parents and Moe Wakaba walking together in a street below the cafe window. Yuno says she cannot recall what it is she has forgotten, but her cellphone has an adornment of the first Muru Muru.
Yuki is seen in the second world, where he is god but the world is nothing more than a void. He believes 10,000 years have passed in the second world, and Muru Muru asks Yuki to do something as she is bored of having only an old and overread manga for entertainment. Yuki says that a world without Yuno would be meaningless, and Muru Muru says he should just create another woman. Yuki however does not care for the idea and merely says that Muru Muruwill understand if she ever falls in love with someone. Muru Muru says she already likes him, but Yuki calmly says he did not mean that. Yuki begins to wonder how the third Yuno is doing and if she's happy, but he has no way to know as the two worlds have been separated. He stares at his Diary while mourning the second Yuno's death.
Then, Yuki's Diary suddenly changes and a new entry is displayed: "Yuno came back to me." With the words "Next Project" appearing next.
- Muru Muru does not put the third selves of Yuno's parents back at home as it was in the manga. Instead, she heals Ushio due to changes in previous episodes.
- Ai and Marco are in an apartment and Ai calls Orin by phone instead of them all being together in the Mother's Home.
- The changes in the future two years after are expanded on or changed from the manga: Hiyama and Yomotsu's changed future is different in the ending scenes, and for the first time in the series Yomotsu's full face is shown. Ai and Marco are enjoying themselves. Reisuke is with his parents playing. Mao, Hinata, Ouji Kosaka and Aru Akise are seen together along with Karyuudo. John Bacchus and Kamado are in some sort of relationship. Tsubaki is shown sleeping happily. Kurusu is happily with his family before being picked up by Nishijima.
- Yuki and Yuno are not seen together although it is mentioned that the two are reunited, but it is never explained how. It is unknown if the words "Next Project" have something to do with it, however in the manga it is shown how they reunite; Yuno smashes the barrier of space and time in order to reach Yuki across a 10,000 year gap between the second and third worlds, Deus then makes Yuno and Yuki the successors of the third world. The first thing that Yukiteru and Yuno do as gods together is to go stargazing in as they create a happy future together.
- A Happy end appears in Yukiteru's diary in the manga, which does not appear in the anime.
- Yuki and Muru Muru are seen with much longer hair after 10,000 years of solitary life.