Yumiko Sakaki attempted to cut Yūji with a blade but fails each time in doing that. He somehow got along with Makina, who is actually quite shy, after he helped her to catch the crayfish. He then visits the principle's office for advice on resolving Sakaki's hostility towards him. He also found out that all of the students, including him, have special circumstances that are sensitive. Yūji's guardian and work boss, JB comes to pay him a visit outside of school. This caused his classmates to question him of JB's identity, especially Amane who is concerned whether Yūji has a girlfriend or not. Later, in the evening, he was ambushed by Yumiko with a blade and he responded by grabbing the hand which is holding the blade. He then tell her that he is not her enemy and intended to be her friend. From that day onwards, Yumiko is no longer hostile towards him and treats him as another student in the academy.

Yuuji suddenly announces that he'll be Makina's father. Everyone around gets confused and looks at them skeptically, but the two of them act like father and daughter very dilligently. Yuuji even becomes a rather Spartan father at the end of the term. He attempts to drive all the knowledge he possesses into Makina, from hand-to-hand combat techniques to marksmanship.

Yūji takes the job JB gave him but only so that he can protect her. To do so, he and Makina leave the Academy so as to present a moving target and Sachi gives Makina an apple sapling as a parting gift. The efforts of the organization to get hold of Makina are fruitless as Yūji is able to dispose of every agent sent after them. As they flee, Yūji becomes aware of Makina's recurrent nightmares involving her father. It is revealed that a few years earlier Makina's father found evidence of the Irisu Group's corruption and was killed in front of Makina on his wife's orders. Makina spent a number of years in a hospital recovering from the trauma. It is further revealed that she has a near photographic memory and had read some of the incriminating documents before her father's death. It turns out that Makina's mother ordered the hit on Makina because she phoned her mother and threatened to reveal the corruption unless her younger sister was kept safe.

When their latest hideout is compromised, Yūji manages to get them away but Makina forgets her sapling. Despite Yūji's admonition to forget about it, Makina returns to the hotel to search for it and is shot. Yūji shows up in time to take her to a hospital but is intercepted by JB. In the hospital, Makina's mother shows up and, to JB's horror and disgust, asks if Makina's internal organs are unharmed because Sarina is in need of an organ transplant. Later, a disguised Yūji shows up at the Irisu Group's HQ and shoots Makina's mother. With the contractor for the hit out of the picture, and with hard evidence of the Irisu Group's corruption in the hands of the organization, Yūji and a recovering Makina return to the Academy.

The international terrorist Heath Oslo uses nuclear weapons as a shield to threaten the nation. The nation plans to make Yuuji a human sacrifice in their dealings with Oslo. There is no other way to save Yuuji from this crisis but to rescue him as he is transferred from Ichigaya to Akasaka.