Araragi Koyomi is a third year high school student who is almost human again after having briefly become a vampire. One day, a classmate named Senjougahara Hitagi, who infamously never talks to anyone, falls down the stairs into Koyomi's arms. He discovers that Hitagi weighs next to nothing, in defiance of physics and common sense alike. Despite being threatened by her, Koyomi offers her help, and introduces her to Oshino Meme, a middle-aged homeless man who helped him stop being a vampire.
March 13th, the morning of college entrance exams. Koyomi Araragi has died due to Izuko Gaen. Mayoi Hachikuji was waiting for him in the afterlife, and guides him towards an unknown destination. Koyomi would have never thought that this certain someone would be waiting for him there.
Koyomi and Hitagi spend the rest of the date bonding further. Once back home, Koyomi has another encounter with Ougi.
Koyomi Araragi has an argument with his sister and then finds it difficult to stay in the house. He goes to the park where he meets Hitagi Senjyogahara. They see a little girl, Mayoi Hachikuji, comparing the town map displayed in the park to the memo in her hand. Learning that Mayoi has lost her way and route to a relative's home, Koyomi offers to help, only to be violently rebuffed.
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.
On the way to school, Koyomi finds Hachikuji in the middle of the street and assaults her in a teasing manner. Hachikuji panics and breaks his finger. Later after they calm down, Hachikuji tells Koyomi that she saw Shinobu at the donut store. Koyomi goes to the school bike rack and gets a text from Tsubasa, asking him to ditch school and come to the playground. He finds her there still in her pajamas and wearing a hat. They begin talking about her recent headaches and Koyomi persuades her to take her hat off. He finds out that she had grown cat ears. They agree to go to Oshino’s place. When they reach there, they find him crouching down, buring something in the dirt. Oshino asks them to come in and hits the side of Tsubasa’s head, knocking her out. Oshino tells Koyomi that she was already half cat. Tsubasa’s hair turns white, and the cat is revealed.
After Koyomi Araragi and Hitagi Senjyogahara discover that the girl they met in the park, Mayoi Hachikuji, is trying to get to her mother's house, they offer to walk along with her. However, they keep getting incredibly lost.
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.
After school Koyomi finds Nadeko and they talk about how Shinobu looked at her and Suruga with a different gaze than Koyomi and Oshino. Tsubasa appears and Nadeko leaves abruptly, Koyomi and Tsubasa talk about how Koyomi has become a bad influence to Hitagi in school. Tsubasa gets a headache and Koyomi flashbacks into what happened in Golden Week, Tsubasa turned into a white "cat-woman" and attacked people by absorbing their vitality. Oshino reveals the problem is because of a huge amount of stress built up over the years. Koyomi acts as bait to attract the cat and Shinobu bites her draining her energy until she turns back into Tsubasa.
The day after his attack, Koyomi goes to see Suruga, where she tells him something about herself he can't quite grasp.
Koyomi takes Suruga to see Oshino in order to help her. However, the help he offers isn't the help Koyomi wanted...
Araragi finishes up cleaning at Kanbaru’s house, and proceeds to head home on his bike. Right outside of Kanbaru’s he sees a strange, ill-omened man, named Kaiki Deishuu who he instantly relates to having a similar aura to Oshino. When he meets Senjougahara on the way home and mentions Kaiki, she chains him up and tells him that Kaiki was one of the conmen that took away her family’s money. When Araragi gets a text from his sister asking for help, he easily breaks free of his chains and Senjougahara lets him go after talking to Hanekawa.
Koyomi Araragi waits in the ruins of the cram school to ask Suruga Kanbaru for help, a request he hopes she will refuse.
Koyomi and Suruga travel to an abandoned shrine in order to perform a favor for Oshino. As they climb the mountain the shrine is located on, they pass a girl running down the path, who only briefly exchanges glances before continuing in the other direction. Once they reach the shrine, Koyomi and Suruga discover a number of dismembered snake corpses in what appears to be some sort of ritual. They both quickly decide to leave. Later, Koyomi comes across Hanekawa in a bookstore, where they begin to converse. Hanekawa warns Koyomi that he and Hitagi must set down boundaries in their relationship if it is to last. She then leaves after getting a sudden headache. Koyomi then meets the girl again, who he finally realizes is Nadeko Sengoku, a friend of his sisters who he met as a child. He and Suruga intercept her at the shrine, and return to Koyomi's house. Once there, Nadeko takes off her clothes, revealing snakelike skin, and pleads for Koyomi to save her.
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.
After Koyomi Araragi catches his classmate, Hitagi Senjougahara, when she fell down some stairs, he makes a strange discovery about her. Trying to keep her secret Hitagi attacks Koyomi. However, he has a secret of his own and might be able to help her.
On his way to Hitagi's house, Koyomi bumps in to Suruga Kanbaru, the school's basketball star and an old friend of Hitagi, of whom he can't get rid of. Later that day, Koyomi is attacked by a mysterious being.
After a hurried departure from the cram school ruins, Koyomi and Suruga head toward the meeting place, only to encounter some difficulty along the way.
To overcome her problems, Hitagi has to face some difficult and painful memories from her past.
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.
Hanekawa reveals her concerns about Ougi as she and Araragi go to visit Oikura.
In the aftermath of the previous day, Araragi is about to enter his classroom when Hanekawa informs him that a student absent all year is finally attending. The story pushes further into the past, as more of “what” makes Koyomi Araragi is revealed.
While Hitagi is off to Oshino for advice, Koyomi learns more about Mayoi's life. When Hitagi finally returns, she reveals some information that surprises Koyomi.
The group relocates to the North Shirahebi Shrine where Izuko Gaen tells them the story behind the location and the effect Shinobu's first minion had on it.
Koyomi is concentrated on his studies when he is interrupted by Karen who, much by his surprise, is wearing her sister Tsukihi's clothes, displaying an air more feminine than usual. Karen asks Koyomi to introduce her to Suruga knowing that she is friends with him, but he refuses without giving a reason, fearing that she would make a move on his sister. Karen then challenges his brother to a contest, making him promise to comply with her request if he loses. Koyomi then choses the contents of the challenge - she would let him brush her teeth for five minutes without resisting, which she accepts. Surprisingly, both start getting more and more aroused as Koyomi brushes Karen's teeth until Tsukihi barges in demanding an explanation. Despite fearing what punishment Tsukihi has in store for them after she leaves and Koyomi accepting defeat, Karen asks him to continue from where they stopped.
Having rediscovered the room on the second floor of the ruined house, Koyomi tells Ougi of the events that happened there five years earlier.
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