One night on her way back from shopping at Kagami Mall, Sakuno Uryū gets lost and she calls her older brother Shingo to come find her. With initially no luck in finding her, and with her cell phone battery nearly dead, Sakuno gets help from a girl passing by, who offers to call Shingo. Shortly afterwards, Shingo meets up with Sakuno and the girl who helped her, Airi Sena, in a nearby park. Shingo, Sakuno and Shingo's friend Hayata Mukunashi, who attend Kagamidai Private Academy, are three of the students chosen in a group to take part in a temporary ten-month transfer to Yuijo Private Academy, which until now has been a prestigious all-girls school. Upon entering the school grounds, they meet Angelina Nanatsu Sewell, a student and maid at the school. Airi forcefully brings her mother and principal of the school to meet the group from Kagamidai, who were waiting for her arrival. Airi makes it clear to Shingo and the others that not all of the students approve of the student transfer and that she is very against the transfer of boys into the school.

After Airi's declaration the previous day, a gloomy atmosphere develops among the Kagamidai students. Shingo realizes that Airi is the only one who can change the current mood at the school. Angelina likes the idea of there being more students around to serve, and one of Angelina's friends, Sana Inui, is also for the student transfer. Shingo makes several mistakes while at school, such as walking into one of the bathrooms with Airi inside, or opening the door of a classroom where girls are changing back into their school uniforms after gym class, which infuriates Airi. During lunch, Shingo meets Miu Amaha, a friendly third-year student who is looking after a strange cat-like creature she has named Pannya. Since there is still much opposition about the male students attending, the principal has them take classes in cooking, learning music, preparing tea and flower arrangement. While making chestnut rice in class, the other boys learn from Shingo's good example and soon the atmosphere changes for the better. After they make too much, the boys offer to eat several helpings and eventually all of the rice is eaten. The next day, Shingo and Airi are chosen as their class' representatives.

Shingo cannot initially get the hang of being a class representative and continues to irritate Airi. Despite Shingo trying to be friendly with her, she makes it clear that she will not be getting along with the boys, and she tells him to leave her alone. Later that night at school, Shingo again encounters Pannya, who leads him to a shed outside with Miu inside. She explains that this is the Nuko Club, which cares for injured animals before releasing them back into the wild; Pannya is one such animal. Miu asks Shingo to join the club. Shingo starts to get used to being a class representative and becomes faster at finishing the work. One evening, Airi has to leave early for a personal matter, and Shingo offers to do the rest of the work by himself, if she will tutor him for the upcoming tests. Airi accepts his proposal, despite her objections. Later, Shingo goes to a local supermarket with his sister, Miu and Angelina, where they unexpectedly run into Airi, who instantly becomes embarrassed.

Airi reveals to her friends that she has been living alone since she entered Yuijo and does not have much money to spend on living expenses. On the way back from the supermarket Shingo and the others stop by Airi's apartment and everyone helps to make dinner. Airi asks them to keep her living situation a secret so as to maintain the way students see her at school. The next day, Airi eats lunch Shingo and the other girls. Airi keeps her promise with Shingo and helps him study for the upcoming tests, as well as Sakuno, Angelina, Miu and Sana. Another day when they are over at Airi's apartment studying, Shingo and the girls celebrate Airi's birthday. While spending more time with the others, Airi begins opening up to them more. After the tests are finished, Airi begins addressing Shingo without the use of honorifics, and Shingo does the same for Airi in return.

Airi realizes her growing feelings for Shingo and she wants to confirm that she feels differently around Shingo compared to other boys. Shingo overhears that the principal is thinking about abolishing the Nuko Club because of complaints from various students. Due to Shingo's constant helpfulness, Angelina starts to see him as her rival in being a maid. When they accidentally bump into each other and her headband is knocked off, Angelina starts to cry and acts very childish. Later, Shingo goes to check up on her and she remarks how he is so attentive and considerate of others. The next day, Angelina runs around school looking for ways to help, but she has no luck in finding any work to do. Airi notices Angelina's downtrodden attitude and goes to cheer her up. In doing so, Angelina runs after Shingo and asks him if he would be her master.

Angelina goes with Shingo and Sakuno back to their house, only to find they have all the household chores covered. Sakuno and Angelina both cook a meal for dinner, and Angelina tries to be as helpful as possible to Shingo later on. Shingo joins the Nuko Club and assists Sana posting member recruitment posters around the school. That night, the principals comes to tell Angelina the student council president is having a hard time without her, and Angelina happily returns to the academy, though she still considers Shingo to be her master. The recruitment posters are taken down and most of them are burned. To help save the Nuko Club, Sakuno and Angelina join and help in the recruitment of a sixth member, which would save the club from abolishment. Shingo and Airi get wet from the rain on the way home, and Airi suggests Shingo come to her apartment to get an umbrella. Airi wants him to take a bath before he leaves, though Shingo is reluctant to take one before her. The two end up taking a bath together with the lights out. The next day, Airi decides to join the Nuko Club, despite being bad with animals.

With now six members, the Nuko Club is officially recognized by the principal. Shingo and the others have to arrive early in the day to care for the animals. Miu invites Shingo and Sana to go with her the next day to buy supplies for the club; Sana is displeased that Miu invited Shingo too. Sana gets upset that Miu and Shingo are now on a first name basis, and that Miu shares some cocoa with Shingo that Sana gave her. Another day, Shingo and Sana are left alone in the club room and Sana applies a compress to Shingo's aching neck. Shingo discovers there is a rumor going around that he and Sana are going out, indirectly due to Miu. Shingo talks with Sana about it, and she says she will clear up the rumor. While Shingo and Sana also get on a first name basis, Sana is still upset with Shingo because she thinks he likes Miu. When in the club room together, Miu falls asleep on Shingo's shoulder.

Sana finds a black and a white kitten abandoned and brings them to the Nuko Club. Since no one can take them home, the club members decide to care for them at the club for now until they find them a home. Shingo and the others ask around, but no one can take the kittens. Shingo notices Miu's wounded fingers and Sana tells him that Miu lets animals bite her to assure them that she will not hurt them. At the same time, Sana asks Shingo what he thinks about Miu. When Shingo comes to school early because of the kittens, he discovers that Miu stayed overnight and slept in the club room to look after them. Shingo asks her not to push herself too hard, as Sana listens from outside. Later on Sana asks Miu the same thing she did with Shingo. After responding, Miu then asks Sana what she thinks about him. Afterwards, the club members realize the black kitten responds to the name Shingo, while the white one responds to the name Miu. The principal expresses her concern about more abandoned animals coming to the Nuko Club, and makes sure the club is taking responsibility for the animals. Shingo tells Miu she should go home after school and get some rest because she has been pushing herself for the animals. When he arrives at the club room, Sana informs Shingo that Miu was suddenly called by her part-time job to fill in for someone else. Shingo goes after Miu to stop her, and he catches her as she collapses on the street.

Shingo brings Miu back to his house to rest for the night, and she goes back home the following morning. To their surprise, Shingo and Sana find Miu in the club room looking after the kittens. The Nuko Club's advisor, Machi Yatsuzuka, places the female kitten Miu with one of her friends, since they could only take that one. Sana volunteers to take the male kitten Shingo home with her, despite Miu's previous protests. Miu invites Shingo to her house because of what happened the day before. At her house, Shingo meets Miu's playful mother, who he at first thinks is her older sister. She tells him that her love of animals stems from a traumatic experience as a child when a pet cat died. After they part ways at the park that night, Shingo returns to Miu's house because he forgot his cell phone, and accidentally sees Miu in the nude as she runs out into the hallway. Miu promises Shingo she will depend on him more, instead of shouldering things all by herself. The next day, Sana runs out of the club room after noticing a difference in how Miu and Shingo act towards each other. Airi stops Sana and suspects that she is upset because of Shingo.

Airi is concerned that Sana is trying to act like she has up until now and ignore that she has feelings for Shingo. At lunch, Sana mentions that the kitten Shingo is not getting used to his new home even after a week's time. The Nuko Club members clean up the club room, and Miu suggests Sana and Shingo go outside to wash a fish tank. When they return to the club room, they find their advisor is back with the kitten Miu, since it also could not get used to her new home. Sana volunteers to take in Miu too, and she leaves to go retrieve Shingo. Airi tries to stop her, but is unsuccessful. Miu tells Shingo that Sana is allergic to cats, which is why Miu was against Sana raising the kitten. Miu also tells Shingo about when she first met Pannya with its mother and later on found Pannya alone and hurt; Miu intends to eventually release Pannya back into the wild. Touched by Miu's gentleness, Shingo tells her that he loves her and as she accepts his feelings, they embrace each other. Sana, who witnessed this, runs off and cries on the swing set while holding the kitten Shingo in the rain. Airi arrives to comfort her and Sana cries on her shoulder.

Sana is absent from school, and Airi covers for her, telling the others she has a cold. Sana comes back on the first day of finals and has dealt with her feelings for Shingo. Shingo studies with Miu at her house for the tests, and they get teased by her mother. Sana suggests she and Shingo go buy a Christmas present for Miu, but Airi is concerned that Sana will just end up hurt. Sana, who still has feelings for Shingo, tells Airi that she would be satisfied just hearing his voice by calling him in the dead of night. In return for accompanying him to buy Miu's present, Shingo buys Sana two cat stuffed animals, one black and the other white. On Christmas Eve, Shingo meets up with Miu after her job is over and they go back to Shingo's house. Meanwhile, Sakuno, Angelina and Sana go to Airi's apartment. Angelina tells the others that she heard a rumor that the school merger is going through difficulties, and in the worst case scenario, there will not be a merger. The girls, lead by Sana, go outside and play in the snow in the nearby park where they talk about love. Back at Shingo's house, Shingo and Miu kiss repeatedly and embrace each other.

Angelina, Airi and Sakuno see what they think is Pannya around town, but soon realize that it was in fact Pannya's mother. The Nuko Club members go to where Miu first met Pannya and see Mamanya (Pannya's mother) and another smaller Pannya-like animal with her. The club members realize they have to let Pannya go back to its family, though this weighs heavy on Miu most of all. Airi is inspired by Miu, who can still smile despite having to give Pannya up, to help the school merger succeed, and organizes a student rally for the cause. Miu tries to be overly happy towards Pannya, but breaks down in the club room and cries on Shingo's shoulder. After talking with her mother, Miu finally resolves to let Pannya go back to its family. The club members go to the forest clearing where Miu met Pannya and it is reunited with its family after the club members say goodbye. Time passes, and in the spring the school merger has been completed. After Miu graduated, Sana becomes the club president. Shingo and Miu spend time together in front of the cherry blossoms. Shingo and Miu return to the forest clearing and see Pannya's tail in the bush.