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.

Early in the morning, after his morning jog, Yūji saw Amane is hacking into his room and immediately intended spy on her to know her intend to do so. He later found that she wanted to give him a morning kiss. Amane then jumped onto his bed and masturbate after smelling his unwashed clothes. He later then make a song for Makina to tease Amane as he, Amane and Makina runs to the classroom for their late departure to the classroom. Amane later then raise her concern on Makina as she is starting to imitate Yūji's actions after they requested Sachi to buy them drink. Later, he heard a voice that sound somewhat erotic and found out that it is from Michiru, who is playing with the cat and lying on the ground. Next day, he was caught into a situation where Sachi is making him a shark pouch with glitters for him and Michiru somehow got him out trouble by giving it to Makina. After that, during their exercise time, he carried Amane to the nurse room to treat her injured leg. Amane then requested Yūji to become her boyfriend and subsequently his older sister. He agreed to the latter proposal. Next day, Amane and Makina take their lunch with Yūji and he then realize that he had been avoiding people since his "master"'s death.

During his morning jog, he met Michiru sitting on the grass with a cat on her lap starring at the sea and had a light conversion with her. Next morning, he saw Michiru drink a 100% Vitamin C drink and later saw Makina and Sachi watching cartoon while doing push ups. Later that night, the rest of people except Michiru discussed about Michihiru and her behavior. Later that night, Sachi, Yumiko and Yūji witnessed Michiru yelled in pain as the hair dye drips onto the floor. Next day in the evening, Amane asked Yūji on the subject of friendship between men and women. When Michiru was asked of it, she run off after responded to it. She became a different person when Yūji found her. She then kissed Yūji after a short conversion and then returns to normal. One morning, after Yūji demonstrated to her what she did to him yesterday, she ran off to calm herself down and chased the cat away. She ended up finding the cat together with Yūji to found out that the cat lying beside the road dying. They went into the cab and witness the cat died as they take a trip on the cab. Michiru then cried while hugging the dead cat.

Michiru tries to run away from reality after losing Meowmel and does something impulsive. Yuuji finds her quickly, and she survives without issue thanks to him. The next day, Michiru acts as cheerful as can be, like what happened the day before was all a lie. She's the same tsundere and idiot as always...

Michiaki Sakaki, Mihama Academy's chairman, makes use of his influence and summons JB to his side. He becomes fed up that the academy he specifically created to put Yumiko, who is supposed to succeed the Sakaki home's headship, in line isn't fulfilling its purpose. He decides to borrow the strength of JB's "company" to do so.

Sachi: the classmate dressed as a maid who will grant any wish. However, to achieve that end she will employ any means necessary. Everyone at the academy knows Sachi has that dangerous side to her, and are careful not to be humble when they speak to her. One day with summer close at hand, Michiru carelessly tells Sachi to make the tests go away while preparing for finals.

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.

JB drops Yūji off at the Academy after a job but before he can exit the car she kisses him on the cheek, much to his discomfort. To complicate matters, he finds that Sachi has witnessed the kiss but promises not to say anything. Yūji returns to his room to find Amane waiting for him. Following their usual banter and a shower, Yūji sits down to dinner when Amane receives a picture of JB kissing him (Sachi took 'saying' literally), which arouses her jealousy. Yūji asks Amane why she is so persistent in pursuing him to which she responds it was love at first sight. He is not satisfied with her answer and presses her. She breaks down and to Yūji's shock mentions his sister's name. She reveals that she and Yūji's sister, Kazuki, were both freshmen on the same basketball team in middle school. As they talk further Yūji finally agrees to allow her to act as his girlfriend provided that he does not have to act as her boyfriend. Amane then retrieves a journal from her room and gives it to Yūji to read. The journal documents the tragic events that befell the basketball team as Amane, the sole survivor, remembers them.