It's the beginning of the second semester and on her way to the first day of school, Tsubasa has a short meeting with Mayoi who reveals that she has just came from Koyomi's house where she forgot her backpack, but could not retrieve it as he was not at home by that time. Soon after, Tsubasa has an encounter with an apparition in the form of a huge white tiger who just passes by her and upon arriving at school she tells Hitagi about it. Hitagi points out that despite Koyomi is for sure be the best person to assist her, Tsubasa did not call for his help at all, also remembering that in fact he always stood for them without the need of asking him. Some time later, Tsubasa and Hitagi watch smoke rising from afar and Tsubasa discovers that her house is on fire. With her house destroyed and no place to sleep, Tsubasa claims to her parents that she will sleep at a friend's house, but she decides to spend the night at the abandoned cram school where Oshino lived instead. Hitagi finds her there upon learning of her situation and decides to take her to her house, suspecting that the white tiger she saw might have some connection with the fire. After deciding to skip school for the next day, Hitagi and Tsubasa receive a mail from Koyomi, where he states that he must leave for a while to deal with some business of his and as they are about to take a bath together, Hitagi asks Tsubasa if she still loves Koyomi. Tsubasa instantly replies that she does.

As her parents still had not found another place to live, Tsubasa keeps staying at Hitagi's place. However, it is later revealed that the recent events had such an impact on Tsubasa that she is once again possessed by the Cursed Cat. The possessed Tsubasa sneaks away from Hitagi's house to confront the tiger she had met previously, as according to her, the fire at her house was caused by it. After a fierce confrontation with the apparition, Tsubasa returns to Hitagi's house just to find her awake and waiting for her. As Hitagi was already aware of the Cursed Cat, she was not suprised upon meeting it. In the next day, Tsubasa is back to normal with no memories of her possession like usual and for some reason, Hitagi asks her once again if she is really in love with Koyomi.

Following her question, Hitagi points out to Tsubasa that despite being similar at willing to help others, she and Koyomi are too different in everything else, including how Tsubasa is too innocent to realize if someone could approach her with malice. On the same day, Tsubasa meets Suruga at the school and learns from her that Koyomi had sent a message to her, and from the message she deduces that he wants to meet her later that night at the abandoned cram school. Upon returning to Hitagi's house, where she meets her father, Tsubasa relays to her what she learned from Suruga, and both agree to not meddle in Koyomi's affairs this time. They are later visited by Karen and Tsukihi who offer their house for Tsubasa to take shelter. Tsubasa accepts their offer, just to later learn that she must sleep on Koyomi's room. In the middle of the night, Tsubasa is possessed again and Shinobu appears before her, claiming that her connection with Koyomi was severed and she is looking for him. The possessed Tsubasa not only reveals about Koyomi's meeting with Suruga, but also offers herself to help her get there faster, but just as the two arrive at the cram school, they find the whole place burned to the ground.

Tsubasa awakens in the next day at the Araragi house and finds out that she was possessed again. As she leaves the house, she is stopped by Koyomi's mother, Mrs. Araragi. The mother explains that while having Tsubasa as a guest is no burden to them, she should not consider the Araragi family as her own. Mrs. Araragi also explains that adverting ones eyes from the truth isn't running away from the problem, mentioning Tsubasa's strained relationship with her own parents. Later, while walking through a park, Tsubasa encounters a man named 'Mr. Episode', who is a half-vampire and once almost killed her. He was also accompanied by a woman named Izuko Gaen, who Meme referred to as his senpai. Gaen claims she knows everything, but surprises Tsubasa when she shows her knowledge on Tsubasa's feelings towards Koyomi, aswell as her tiger problem. Gaen and Mr. Episode depart, after saying that Tsubasa's problem is her own, and only she can solve it. Tsubasa goes to the library to research "Kako", what Gaen called the Tiger, but finds nothing. She calls Hitagi, whom expresses her concern that Gaen named the Tiger "Kako" herself, to learn that Gaen was the maiden name of Kanbaru and her mother. Hitagi then explains that Tsubasa and the burnings are linked, as wherever Tsubasa sleeps, the place burns down soon after, which may eventually include Hitagi and Koyomi's houses. Tsubasa returns to the Araragi house, to be forced into a game of cards with Karen and Tsukihi. They discuss what the words "fire" and "flame" mean, and the sister's boyfriends. Tsubasa explains that Koyomi refuses to acknowledge the sister's boyfriends because of envy, then realizes that she is being jealous. As she prepares to confront the tiger, Tsubasa believes that she may never be able to see Koyomi again, and after attempting to leave her own mark in Koyomi's room so he remembers her, she takes a picture of herself and sends it to someone, and writes a note to her other self, in hopes that they can share

In her letter to the cat spirit, Tsubasa reveals that just like her, Kako is another apparition sired by her repressed feelings, this time of jealousy and asks her to return both to her heart, as she is finally determined to shoulder all of her negative feelings no matter how it will change herself. As Kako is about to burn Hitagi's apartment, Tsubasa appears to confront it. Despite having no chance to defeat Kako, Tsubasa manages to stall it long enough to Koyomi to appear and defeat it with Heartspan. Before absorbing both the cat and tiger spirit, Tsubasa finally confesses her love for Koyomi, and as expected, he rejects her, assuming that his love for Hitagi is stronger. After her family finally rents another house for them to live, it is revealed that Tsubasa's hair developed white stripes just like a tiger, that she hides by dying them black, and she had at last asked her parents for a room just for herself, as a sign that she finally had become a true member of her own family.

On August 20th, Koyomi Araragi left his home to deliver to Mayoi Hachikuji something she had forgotten, and bumped into the young shikigami girl Yotsugi Ononoki. Koyomi ended up buying Yotsugi a popsicle but was unable to find Mayoi. He realized upon coming home that he had not done any of the homework that he was supposed to do, yet tomorrow was already the day of the term opening ceremony.

Realizing that he traveled to a day before Mayoi's death, Koyomi decides to save her and prevent that she becomes a ghost. While looking for directions, he and Shinobu meet a six year old Tsubasa who, suspicious of him, points them to the nearby police station where they learn Mayoi's address and return in the following day planning to guide her safely to her mother's house, but after hours of waiting, Mayoi's father appears and they learn from him that she had left home early in the morning. Koyomi manages to meet Mayoi at the same place where they first met, but after scaring her away, he saves her from being hit by a truck and his plan to prevent her death succeeds. However, after returning to the present, Koyomi realizes that his actions changed drastically the course of history as according to him, it led the world to its destruction.

Returning to the present, Koyomi and Shinobu find the whole city deserted and it does not take long for them to realize that it was a consequence of saving Mayoi's life in the past. Based on the date of the most recent newspaper they found, they come to the conclusion that something dire happened during the events of "Tsubasa Cat" and return to the shrine to look for a way to return to the past. However, they find that Oshino had put a different charm that prevents them from using its powers and when night falls they are surrounded by undead beings. After escaping, Shinobu realizes that the undead were once vampires who lost their master, and that said master must be no other than herself. According to her conclusions, when Shinobu ran away from home, it was Mayoi who helped Koyomi find her, and as she did not become a ghost in the current timeline, she had never become friends with him, thus he did not manage to find Shinobu, leading him to be killed by the Cursed Cat and Shinobu starting a worldwide vampire infection before killing herself. Looking for survivors, Koyomi and Shinobu decide to use some fireworks to bring the attention of whoever managed to escape with their lives, but it ended drawing the undead to them once more.

A woman appers to drive out the undead by throwing rice at them. Much to his awe and joy, Koyomi learns that the woman is none other than Mayoi herself, bringing him a letter from Oshino, who somehow figured out the whole situation. From the letter, Koyomi and Shinobu learn that they had traveled to a different timeline and before they return to their unchanged, original timeline, he asks them to confront Shinobu's alternate self who is still alive, and must be destroyed to stop the undead plague and prevent the world from being destroyed for good. After bidding farewell to the adult Mayoi, the pair return to the temple ruins and meet the alternate Shinobu, who cries of joy upon seeing that in another timeline, she managed to reunite with Koyomi, and offers to sacrifice herself to allow them to return to their own timeline. Back to their own rightful time, Koyomi realizes that he missed the opening ceremony much to his chagrin, and after Shinobu returns to his shadow, Mayoi appears before him, and they take their time as they walk together to his house in order to return her backpack.

Fully transformed into an aparition, Nadeko confronts Shinobu and a battered Koyomi who attack with the intention of killing her, and envious of their relationship, she stabs Koyomi's heart. The story then retrocedes to some days before, in Halloween, when Nadeko, on her way to school has a short encounter with Ougi Oshino, Meme Oshino's nephew, who is also a first year student Koyomi's high school. For some reason, Ougi claims that it is about time for Nadeko to stop always playing the victim before she leaves. At her school, Nadeko starts having visions of white snakes and calls Koyomi for advice, and they agree to meet at 10 PM at his house, as by that time Shinobu must be awake to provide some help. Soon after, Nadeko hears the voice of a snake instructing her to meet it at the shrine where she used to kill snakes instead and there it reveals itself as the giant apparition snake, Kuchinawa, who demands compensation for its fellow white snakes she killed by asking for a favor, to which she agrees.

After lying to Koyomi claiming that she was just imagining things, Nadeko decides to help Kuchinawa find his lost corpse, but they agree that she will attend school as usual, while looking for his body at night. In the next day, during school, it is revealed that Nadeko's class is still in a bad mood due to the incident with Kaiki's charms, and thus the position of class rep was somewhat forced on her. Later at night, Nadeko sneaks out of her room to start looking for Kuchinawa's body and after following a false lead, she is found by Koyomi, who takes her to his house. It is then revealed that Nadeko's parents had realized she was missing and contacted Tsukihi, who lied to them claiming that she was sleeping there, while Koyomi left to look for her. After insinuating to Nadeko that they should sleep together, Koyomi is knocked out by Shinobu who appears before her and ponders on how convenient it is for her to have such a cute and defenseless demeanor before she drags Koyomi away to have him sleep on the couch.

Nadeko awakens in the next day with Tsukihi, who had sneaken into Koyomi's bed with the intention of sleeping beside him, at her side. In the occasion, Tsukihi has Nadeko confess that she always was in love with her brother and realizes that the reason why she still harbors feelings for him it is because it makes easy for her to reject all other boys who ask her out, as she believes that having a proper relationship is too bothersome. Following that, Tsukihi then grabs a pair of scissors and cuts out Nadeko's bangs, claimimg that she is doing her a favour. Later at school, Nadeko's homeroom teacher keeps pressuring her to help him restore the mood along her classmates, but when she tries to ditch him out as usual, she realizes that without her bangs, her face is fully exposed, preventing her from hiding her true feelings and suddenly, she vents out her anger at him for pushing all his work on her and following that, she lashes out at her classmates for refusing to make amends with each other after the charms incident. After school, Kuchinawa reveals that Nadeko's sudden change of behavior is because his presence made her show her true feelings which she usually keeps repressed and claims that he discovered that what he wants Nadeko to seek for him is hidden in Koyomi's house. Nadeko then sneaks there and searches Koyomi's room until she finds a talisman and Kuchinawa, revealing that it is what he was looking for, asks her if she has any wish he could grant her as an act of gratitude. Nadeko then reveals that her wish is to have her feelings for Koyomi become requited, but Koyomi himself steps into the room and asserts that it is not possible.

Despite Koyomi's warnings, Nadeko swallows the talisman and revives Kuchinawa after Shinobu berates her for once again playing the victim. The story then shifts forward to Nadeko's confront with Koyomi and Shinobu at the abandoned temple and it is revealed that she defeated both. Kuchinawa then reveals that he had met Nadeko when she swallowed the talisman and all their previous iteractions were fruit of Nadeko's own imagination. It is also revealed that it was Ougi who had filled Nadeko about the talisman's location and that all her movements since then were a ploy to infiltrate into Koyomi's house and secure a key to break into there in secret. As Nadeko is about to kill Koyomi, she answers a call from Hitagi at his phone. Hitagi then reveals that Nadeko must kill her, Shinobu and Koyomi at this order or she may end up being killed by either Hitagi or Shinobu, and in exchange for this information, Nadeko agrees to return to kill them all at the day of their graduation. Six months later, the day of graduation is at hand, and Nadeko waits at the polar snake shrine for Koyomi, Hitagi and Shinobu, who accompained by Suruga and Tsubasa, appear to confront her.

After returning from his trip through time, Koyomi returns home and after he returning Mayoi's backpack, they come across a mysterious being that starts chasing them down. The two manage to escape when they meet Yotsugi who flies away with them to safety. After stealing a kiss from Koyomi to repay for her help, Yotsugi flees, leaving Koyomi at the mercy of a furious Shinobu that appears soon after and to calm her down, Koyomi kisses her too. With Mayoi still uncounscious from their predicament, Koyomi inquires Shinobu about the "darkness" entity they saw and she claims that she had seen it before during a trip to Japan 400 years before. She also claims that it will cause the destruction of the entire city if nothing is done about it.

Shinobu reveals that during her first visit to Japan, 400 years ago, she saved the local people from a severe draught by accident and was revered as a goddess by them. She then spent the next years living as a goddess in Japan until all the villagers started disapearing mysteriously, until only Shinobu and a demon hunter she befriended remained. Soon after, the same being that Koyomi met attacked them and Shinobu barely escaped alive, taking with her the demon hunter's hand by accident, which she used to revive him as a servant of hers just like Koyomi. However, the man blamed her for all that happened and unable to reason with him, Shinobu watched him commiting suicide by exposing himself to the sunlight. Since then Shinobu never returned to Japan until six months ago, when she and Koyomi first met.

After Shinobu tells Koyomi her story, they realize that Yotsugi was overhearing their entire conversation and after Mayoi awakens, they start discussing ways to deal with the darkness being before it appears before them. Koyomi, Mayoi and Yotsugi manage to escape again, but Koyomi is knocked out cold by the shock of Yotsugi's jumping just to awaken several hours later and learn that they unwillingly left Shinobu behind. As Koyomi's vampire powers had not disappeared yet, they conclude that Shinobu is still alive but with Koyomi's powers weakening, it means that they have to find her before she is killed for good. Having no clue about what to do, they decide to contact Izuko Gaen who might provide some advice and when they decide to take shelter in a house, Izuko herself opens the door for them, much to their surprise.

In exchange for her help, Gaen requests three tasks from Koyomi, all being connected to Suruga Kanbaru, formerly known as Suruga Gaen. Izuko reveals herself as her aunt, but she doesn't want to be introduced to her as one, because she cares for Suruga's feelings. When Koyomi accepts, she shows the darkness' true motive - it is after apparitions not behaving like they should, and this time it isn't after Shinobu, but Mayoi. She exposes Mayoi as a "ghost of a ghost", who should have passed on on Mother's Day, when she finally found her way home; she also stopped leading people astray, neglecting her duty as a lost cow. After Gaen leaves, Mayoi realizes she has to pass on, rather than be eaten by the darkness, and thus she bids Koyomi farewell by kissing him and telling that she loved him. Four months later, Koyomi tells the story of the incident to only one person - Ougi Oshino. On his way home, he realizes he never told Mayoi one thing he should have said - goodbye.

On New Year's Day, Kaiki receives a call from Hitagi requesting for his services. After claiming that he is in Okinawa in an attempt to shake her off, Hitagi affirms that she will take a flight to meet him there, forcing him to do the same to keep his lie from being exposed and Hitagi from killing him. Once meeting at the airport, Hitagi explains their problem with Nadeko - she wants him to deceive her into letting them live as the day of their graduation and battle with her approaches. Despite seeing how Hitagi is desperate enough to resort to asking a man she loathes and that she is prepared to attend whatever demand he asks, Kaiki claims that he has no reason to help them at all before considering their connection with Gaen's niece Suruga, causing him to accept Hitagi's request.

Kaiki decides to help Hitagi for a mere ¥100,000, much to her surprise. They leave Okinawa on separate flights to not arouse any suspicion. Posing as the father of one of Nadeko's classmates, Kaiki infiltrates her home to search for any clues. Kaiki discovers several suspicious details, such as the fact that Nadeko had only photos of herself without any friends and that her parents, apparently not curious as to the cause of her disappearance, never opened Nadeko's closet as she requested. Kaiki determines that she was a very spoiled child. After a brief phone conversation with Hitagi, Kaiki decides to visit the Polar Snake Shrine to learn more about Nadeko. Immediately upon Kaiki making a donation at the shrine, a mysteriously cheerful Nadeko appears. Apparently, Kaiki is her first visitor, despite Nadeko's best efforts at renovating the shrine. Kaiki asks her several questions about her relationship with Koyomi, confirming her twisted conception of unrequited love and that she still means to kill Koyomi and Hitagi. Kaiki takes his leave after giving Nadeko some yarn for cat's cradle to occupy her time, promising to return before she perfects any patterns.

Returning from his visit at the Polar Snake Shrine, Kaiki asks Hitagi to meet him again, ending up in a Mister Donut restaurant. Kaiki claims that it will be easy for him to deceive Nadeko as at her current condition, she can't doubt anyone - she has turned even more childish than she was in her human state, unable to detect any ill will. He reveals his plan to spare Koyomi and the others by lying to her that they died in an accident, thus he needs Hitagi to convince Koyomi to cease all connections with Nadeko. Hitagi, relieved and crying, thanks him for his services. On the following day, Kaiki is approached by Yotsugi who comes with an ultimatum from Gaen urging him to pull off his scheme to deceive Nadeko, claiming that the stake is too high and the entire city may be destroyed should he fail. Despite accepting ¥3,000,000 as compensation from Gaen, Kaiki moves on with his plan and pays another visit to Nadeko, claiming that he has a special wish she can fulfill and he will keep visiting her in a 100 visit cycle. Nadeko cheerfully tells him that she destroyed the cat's cradle yarn and used a white snake instead. Terrified, he determines she is not only an idiot, but also insane. After the meetup, Kaiki tricks Nadeko's parents to have them leave their house and he takes the opportunity to investigate her room, getting startled upon finding out what she kept hidden inside her closet.

Kaiki returns to his hotelroom and finds an envelope with an anonymous message telling him to pull off. After tearing it up and flushing it in the toilet, he contacts Hitagi, telling her about the incident with Gaen and Yotsugi. He asks her if anyone else could profit from having him stop his plans to deceive Nadeko, however she has no idea who could have such goals. She asked if she could see the message, but Kaiki noted that he destroyed it already. Before hanging up, Hitagi warns him to beware of Nadeko. On the following day, Kaiki pays another visit to Nadeko just as promised, but this time he offers ¥20,000 and a bottle of sake instead of the usual ¥10,000, much to Nadeko's joy. Returning from the temple, Kaiki is approached by Hanekawa who wants to talk to him. As they return to the city on a cab, Hanekawa reveals that she had just returned from her search for Oshino overseas without Hitagi's and Araragi's knowledge and even though she knew that continuing to look for him is futile, she intends to depart again on the following day. It turned out that Gaen personally warned Hanekawa to stay out of the intrigue. She invites Kaiki to her hotelroom. Kaiki, after making sure she is on their side, suggests her to exchange information with him.

Kaiki learns from Tsubasa that strange phenomena have been happening in the town even before Shinobu arrived and because of that, Gaen was intending to have her become the new god of the Polar Shrine. However, because of Koyomi's interference, her plans have failed and Nadeko turned into a god instead. Tsubasa believes that Nadeko actually does not care about anything or anybody at all, and most likely doesn't really love "Big Brother Koyomi", thus the reason for her behavior. She is also worried if Kaiki is able to pull off the scam. On the occasion, Tsubasa asks Kaiki if Oshino has any relatives like a niece and he affirms that just like him, Oshino does not have a family at all, including siblings or such, making the existence of Oshino Ougi very suspicious. Through the following days, Kaiki keeps visiting Nadeko to play with her and bring her presents until the day of Koyomi and Hitagi's graduation finally arrives. After having a final conversation with Hitagi by phone, during which she demands him to never set foot in the city again once the job is done, Kaiki has a short meeting with Yotsugi on the way to the shrine. She repeats her warning and claims Kaiki won't be able to deceive Nadeko. On the occasion, it is revealed that Kaiki used his wits to bring down a cult that was deceiving Hitagi's mother but that ultimately led her to join another cult instead and for Hitagi's sake, he had her mother divorce and leave her family. Upon meeting Nadeko at the shrine, Kaiki attempts to deceive her as planned by claiming that Koyomi, Hitagi and Shinobu were killed in a traffic accident in the previous night, however, she instantly recognizes the lie.

Kaiki realizes that he failed to deceive Nadeko because she never trusted him at all, and because she was previously deceived by Ougi into claiming the charm and becoming a god. Nadeko unleashes a swarm of snakes onto the entire Polar Snake Shrine, immobilizing Kaiki. Believing that he was sent by Koyomi, she contemplates killing his sisters, Kanbaru, Hanekawa and Mayoi as well to punish him, until Kaiki reveals that he found out her secret aspiration to become a manga artist, as many drawings were hidden in her private closet. Embarassed for having her secret revealed, Nadeko starts punching and kicking Kaiki as he tries to persuade her. He claims that eventually her parents will open the closet as well and find out about her secret, unless she renounces her godhood and returns home. After convincing her that she should forget about Koyomi entirely and pursue her true ambitions instead, she agrees to get deceived again. Kaiki implants a fake slug apparition into her body to have her uncounscious during the exorcism, but he's interrupted by Koyomi rushing into the shrine. Claiming that he was sent by Gaen as a professional to deal with Nadeko, Kaiki extracts the snake charm from her body and returns it to him. Kaiki also instructs Koyomi to cut all connections with Nadeko for her sake, as she must move on with her life by herself - his relationship and romance with her would only make her an useless human being. After calling Hitagi and confirming that his job is done, Kaiki bids farewell to her and realizes that the secret message at his hotel was sent by no other than Hitagi herself, as she knew it would have him push further with his job instead of discouraging him, and Gaen's message to him probably was for the same purpose. As he leaves the city, Kaiki is ambushed and mortally wounded by one of the boys he formerly deceived, possibly the one who cursed Nadeko, and before he passes away he hears Ougi's name, implying that he was sent by her.