Following an encounter with oddity specialist Izuko Gaen, third-year high school student Koyomi Araragi wakes up in a strange, deserted void only to be greeted by a joyfully familiar face in an alarmingly unfamiliar place. Araragi, with the help of his girlfriend Hitagi Senjougahara, maneuvers through the webs of his past and the perplexities of the present in search of answers. However, fate once again delivers him to the eccentric transfer student Ougi Oshino, who brings forth an unexpected proposal that may unearth the very foundation to which he is anchored. As Araragi peels back the layers of mystery surrounding an apparition, he discovers a truth not meant to be revealed.

The story centers on Koyomi Araragi, a third year high school student who has recently survived a vampire attack, and finds himself mixed up with all kinds of apparitions: gods, ghosts, myths, and spirits.

Surviving a vampire attack, meeting several girls plagued by supernatural entities, and just trying to get through life are some of the things high school student Koyomi Araragi has had to deal with lately. On top of all this, he wakes up one morning to find himself kidnapped and tied up by his girlfriend Hitagi Senjougahara. Having run afoul of Deishuu Kaiki, a swindler who conned Senjougahara's mother, she has taken it upon herself to imprison Araragi to keep him safe from the con man. But when Araragi gets a frantic message from his sister Karen, he learns that the fraud has set his sights on her. Along with Karen's troubles, his other sister, Tsukihi, is having issues of her own. And when two mysterious women who seem to know more than they should about Araragi and his special group of friends step into their lives, not even he could anticipate their true goals, nor the catastrophic truths soon to be revealed.

Tsubasa and Hitagi discover that Koyomi has gone missing and has urged them in a text message not to look for him. However, in his absence, new dangerous apparitions begin to appear and target Tsubasa, and Nadeko who are left to try and deal with them on their own. Meanwhile, Koyomi Shinobu, and Mayoi are dealing with serious problems of their own.

During the month of October of his third year in high school, Koyomi Araragi is introduced to a transfer student named Ougi Oshino by his underclassman Kanbaru Suruga. Ougi tells Koyomi that she has something she wishes to consult with him. When she draws the map of Naoestu High School, she finds something peculiar on there. This discovery reveals a tale that wasn’t meant to be told, and this makes Koyomi’s high school life totally different. This is the story that brings to light “what” makes Koyomi Araragi. This is the story that reveals the “beginning” of everything.