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Upon visiting her friend, Run, to tell her she managed to get into her high school, Tooru finds her in a compromising position with one of her classmates, Yūko, who Tooru takes an instant disliking to. School soon begins, with Tooru showing hostility to anyone who gets too close to Run, and Yūko and their other friend, Nagi, making sure Run doesn't hurt herself with her aloofness. After school, Tooru admits she feels lonely being in a separate class from Run, but Run assures her that nothing's changed between them.

Run gets into a little trouble when she forgets to put on her underwear in the morning. Yūko goes into a little panic when Run collapses, though it turns out to be just a bit of sleep deprivation. After having to deal with heavy rain, the girls spend the evening at Nagi's house to dry off. While Run and Nagi take a bath, Tooru forces Yūko to sit through a scary movie before continuing to tease her during their bath time. A little while later, the girls leave with some umbrellas they borrowed, but soon return after Yūko gets herself dirty again.

In her first year class, a classmate named Yutaka becomes overly friendly towards Tooru, which bothers her a bit. Meanwhile, a new health teacher, Mr. Satō, becomes attracted towards Run due to her forehead, which naturally bothers Tooru. It is later revealed that Satō is physically weak himself. As Yutaka becomes increasingly clingy to Tooru, her friend Miho tries to keep her in check, though this admittedly makes Tooru feel lonely.

As the students clean the school up, Miho gets to know Tooru, much to Yutaka's chagrin, while the other girls have some fun cleaning the pool. Later, Nagi becomes concerned that she's gaining weight and goes on a diet, but is later convinced that she shouldn't force herself to do so.

After noticing the first years hanging around the pool, Run suggests a trip to the beach for summer vacation. Yūko and Nagi go swimsuit shopping, while Run gives Tooru her swimsuit from elementary school, do to Tooru's small stature. They soon arrive at the beach, where they have fun playing in the sea and sand.

Run ends up giving Tooru an undesirable haircut, but manages to fix it into something she appreciates. Tooru has trouble dealing with her erratic teachers while Yuko mistakes Yutaka's way of dusting out her neckerchief as a cry for help. When Yuko forgets a form she needs to fill in at school, the gang decide to sneak into the school at night to retrieve it, as well as do some exploring. As Nagi and Yuko go to the bathroom, they spot a strange glow outside, which they later discover to be Mr. Satō who then collapses, forcing the others to carry him to the nurse's office. At the end of the day, Yuko still forgets to collect her form.

The girls go to a karaoke bar, where Tooru is nervous about singing in front of Run, but Run helps her out by singing a duet with her. Later, the girls go to a matsuri festival, where they become so engrossed in one of the stalls that they almost miss the fireworks.

As summer vacation ends and school resumes, Tooru's homeroom teacher, Ms. Kito, is unusually energetic. Meanwhile, Yutaka continues to harass Tooru, with Miho explaining why they became such fans of her. Later, Tooru and Run end up having an argument, which lead their respective friends to become concerned for them the next day. As Run notices that Tooru had anonymously bought her a drink, she finds her on the roof where they make up with each other.

As Halloween approaches, the girls decide to hold a small get-together. Nagi receives a strange plush doll from Run, which she has trouble identifying. While Run and Yūko attempt to make food for the party, with messy results, Tooru and Nagi go to buy some snacks, where they find a dirty manga with a heroine that looks like Yūko. After Run's failure at trying to make hotcakes from a mix, the girls decide to make some together from scratch.

As Winter settles in, Tooru finds an abandoned kitten and decides to take care of it. After showing the cat to the others, Tooru goes with Run to visit a pet shop and a family restaurant, where Run comes with a name for the cat, Tansan. The next day, snow falls at school and the students have fun playing in the snow, except for Nagi who is noticeably bothered by the cold. By the next day, however, everyone but Nagi catches colds.

As Tooru's birthday approaches, Run remembers how Tooru helped her study for her high school entrance exams two years ago. Run brings in some cake into school for Tooru's birthday, some of which she spikes with wasabi. As they go home that day, Tooru starts to worry that at the end of the next school year, Run will graduate.