Conan tranquilizes Sonoko and begins the deduction. It turns out that the desk and chair were taken out to the yard when it was raining, and the footprints are missing because the rain was so heavy that it quickly deformed them. The piece of paper was dry because an umbrella was covering it, and the umbrella had long, thin ropes attached to it, which allowed the culprit to quickly retrieve it after the rain without the need of stepping in the yard. The strange traces on the ground are evidence of someone dragging the umbrella, and the water droplets in the hallway are there because the culprits attempted to dry his umbrella by shaking it. But since this does not completely dry the umbrella, water will accumulate under it over time. The culprit is therefore Kunishige Seko. Araide asks how Seko can prevent people from getting suspicious by seeing an umbrella in the yard, and Conan replies that the view is blocked by trees on the first floor and that on higher floors people would think that the headmaster is carrying out his tradition again. Also, since he knew that he would be alone in the nursery for the whole afternoon, he could enter and leave it freely.
Conan further explains that the first haunting event happened because Seko was in the storage room at the time. The second happened because Seko and Hosaka were childhood friends, and therefore Seko would know what Hosaka was interested in and could easily find books that he read despite their obscurity. And the third happened because Seko hid ice in the fire extinguisher embedded in the wall beside the stairs so that it could melt during the night to form a large amount of water the next morning. The wax there was placed against the wall to form a ramp, which would prevent the water from being too near to the wall (this thus prevented people from making a connection between the water and the fire extinguisher).
Seko admits that he was behind all of these events and exclaims that he did so because he believes that Hosaka was bullied and died because something pushed him off the stairs, and that creating rumors about ghosts haunting the school will frighten the bully so that Seko finds out who he/she is. Momobe rejects Seko’s inferences and says that Hosaka was not bullied to death, and that if anyone were to be blamed it would be him. He explains that one day, when trying to carry heavy sculptures into the art room, he fell down from the stairs, and Hosaka, who was behind him and trying to save him, was unfortunately crushed by Momobe’s body and the sculpture.
Seko is unwilling to believe any of this, and retorts by questioning why Hosaka’s desk and chair are left in the lightless storage room. Tsukamoto, who was in the same class as Hosaka, explains that it was to preserve his belongings as he was gone. She says that her classmates unanimously agreed to not give the desk and chair to someone else so that on graduation day, they can bring them out and place them with the desks and chairs of everyone else, making it appear that Hosaka has always been with them and will graduate together with them. Their teacher initially was reluctant to put the perfectly functional desk and chair into disuse, but consented to storing them in the storage room after her classmates collected enough money to buy a new desk and chair. Araide intervenes by saying that he was the doctor who first arrived after Hosaka’s serious injury, and that he heard Hosaka joke about the accident. These words abate Seko’s fury, clear up his previous misunderstandings and make Momobe feel a bit better about the accident. Araide later admits that what he said is a white lie.
After parting from Conan and the highschoolers, Araide receives a phone call from Jodie. Jodie asks him about his re-integration into Teitan High School, and Araide says that it has been quite good thanks to her briefing on Vermouth’s actions. Jodie then tells him to forget about the FBI, and that they will not be in contact in the future. Araide asks whether Vermouth is really a very bad person, as multiple students and staff showed high regard for Dr. Araide’s personality and medical knowledge during the impersonation. Jodie sharply rebukes Araide by using an insult and roaring that nobody who can keep smiling as they kill someone can be good; then she hangs up. Jodie then thinks to herself that Vermouth has the frightening ability to imitate even the personality of her target, and that Araide is too kind and good-natured.