A young man walks a distance of 175km and moves to Mishima Cape with a single backpack on him: Yuuji Kazami. The wish of this man so free from worldiness was thus: "I want to enter an ordinary school and lead the life of an ordinary student."

At first Makina is scared of Yuuji and hides behind Amane's back, but she gradually opens up and starts to get attached to him. While all his classmates deepen their friendships with Yuuji, just one remains on guard against him: Yumiko Sakaki.

One day while having fun with her classmates, Amane sprains her leg during PE. Mihama Academy has no resident nurse, so Yuuji, who learned first-aid at his previous school, treats her injury. While he tends to her, Amane confesses how she feels and says "Be my boyfriend." It's so sudden Yuuji comes to the conclusion she's teasing him. Amane says in response, "If you won't be my boyfriend, then I'll be your big sister!"

Yuuji notices Michiru walking along the path to the high ground which overlooks the sea while on his daily, early morning run. He gets curious and follows her. There, Michiru reveals an enervated side to herself so lacking in her usual energy and asks, "What happens to people when they die?"

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.

Yuuji is urgently summoned to headquarters by JB only to find an assassination directive for Makina Irisu waiting for him. Makina is the eldest daughter of the Irisu family which controls the country from behind the scenes, and knows all of its dark secrets.

Amane has shown one-sided favor for Yuuji, who she should have been meeting for the first time, ever since the day he transferred in. Yuuji is left wondering if there isn't a more compelling reason she is always so devoted to him other than "love at first sight," even though it hasn't been long since she got to know him.

The Takizono basketball club members who have narrowly survived the bus' fall can't reach anyone for help. They've been left behind in what seems like Hell on Earth. In the middle of that hopeless brush with death, Amane meets a girl who calls herself "Kazuki Kazami."

It has been several days since falling into the abyss. The girls exhaust their food on hand and don't have the willpower left to believe they'll be saved. Slowly but surely they begin to break.

With Yuuji's encouragement, he and Amane decide to go face their past together. However, Yuuji does have one doubt about Amane's story: "Did Kazuki really die?" Yuuji heads to the accident site with Amane leading the way to find answers.