Koyomi and Ougi find themselves trapped in a classroom, and the story shifts back to the point when Suruga introduces Ougi to Koyomi. Ougi approaches him with a mystery about a room not seen in the school's blueprints for them to investigate. When they enter the room, they find themselves trapped inside, leading them to their current situation. While talking about their predicament, the duo realize that the room is an oddity created by a traumatic memory from Koyomi's freshman years. Koyomi then tells Ougi that two years prior, the class president at his and Hitagi's class at the time, Sodachi Oikura, was looking for possible culprits of cheating on a math test, and would not allow any student to leave class until a culprit was found. Ougi surmises that they themselves won't be able to leave the room until the two-year-old mystery is solved.

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.

Having rediscovered the room on the second floor of the ruined house, Koyomi tells Ougi of the events that happened there five years earlier.

Hanekawa reveals her concerns about Ougi as she and Araragi go to visit Oikura.

Araragi and Hanekawa visit Oikura and learn the painful story of her family's past.

Ougi claims to have figured out the whereabouts of Oikura’s mother and, in her own way, helps Araragi and Hanekawa to solve the mystery.

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.

Having finally arrived at the meeting place, Koyomi and Suruga find an unexpected person waiting for them. Before their reunion can take place, they must face an unexpected foe!

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 confronted by Shinobu's first minion, the original apparition killer. But instead of starting a battle, the samurai makes a simple request.

As Koyomi prepares for his duel, he learns of the crisis that Hanekawa is facing and must decide what battle he should fight.