After Yūto Ayase returns an anime magazine to the school library, he accidentally runs into the most popular girl in school, Haruka Nogizaka, and discovers her secret that she is an anime and manga otaku which greatly distresses her. Haruka starts avoiding Yūto at all costs which causes others around them to blame Yūto for doing something bad to her. Eventually, Yūto finds Haruka on the school roof where he explains that he will not tell anyone about her secret hobbies if she does not want anyone else to know. This makes Haruka very relieved and happy that if anyone had to find it that it was Yūto.

Yūto and Haruka start spending more time together, such as walking to school together, which causes their peers to get annoyed that Haruka would be hanging out with someone like Yūto. Haruka asks Yūto to accompany her to Akihabara on Sunday and he agrees. The two spend most of the day going from store to store looking at the goods but not buying anything, though Haruka wastes some money on a toy vending machine. Yūto and Haruka even go to a maid café for lunch where Haruka is dressed in a pink maid uniform and gets her picture taken with Yūto. At the end of the day, they discover the handheld gaming console Haruka had intended to buy was sold out for now. This distresses Haruka, but Yūto cheers her up later by assuring her that he had a good time today with her.

The day before a test, Yūto comes over to Haruka's mansion and meets her younger sister Mika and two of her maids, Hazuki and Nanami. The next day at school, a guy bumps into Haruka which causes her bag to go flying which also exposes the Comiket catalog she had. Yūto manages to make everyone believe the catalog is actually his and Haruka only picked it up, though after this Haruka does not come to school for three days. He goes to see her where he finds out from Mika how her secret was exposed during middle school and she had to transfer schools due to being isolated from her peers. Yūto assures her that he will never leave her which relieves her so much that the next day she affirms after a short conflict that the catalog is actually hers.

Yūto, Haruka, Mika and Nanami become increasingly worried about Hazuki's attempt to distance herself from the family and thus decide to follow her on a shopping trip, meeting up with various familiar faces like Yūto's otaku friend Nobunaga, Yūto's sister Ruko and their teacher Yukari. Mika and Nanami eventually becomes distracted in buying lingerie, leaving Yūto and Haruka to the job and almost came to a conclusion that Hazuki was about to get married and quit her job. Before going home, they had a misunderstanding with a bridal shop where they are thought to be customers and were given a chance to take a portrait together with Yūto wearing a tuxedo and Haruka in a wedding dress. That night, Hazuki, much to everyone's relief, explains that she is not quitting, but was just going to a hardware store, which was located above the bridal shop, to fix her chainsaw.

The girl Yūto already bumped into twice turns out to be Shiina Amamiya, the new transfer student into his class. The school swimming tournament is coming the following week, but while Shiina can do an arrange of other skills, swimming is not one of her strong points, so Yūto and Haruka help her prepare in the school pool, but Yūto's sister, and Haruka's sister and maids come along too. At the tournament, Shiina gets a leg cramp during the race and Yūto jumps in to save her, and he takes her to the infirmary. She was not seriously injured, and was more shocked than anything else; Yūto reassures her that she tried her hardest, and that is what matters.

Yūto and Haruka attend the summer Comiket convention together, but since it is the first time for both of them, they underestimate the massive scale and hoards of people who attend. Mika, Hazuki, and Nanami tag along in disguise and help Haruka obtain a dōjinshi she wanted, and to get her out of trouble when people started taking pictures of her. Yūto and Haruka grow closer throughout the day, but after he leaves her at her house, Yūto is asked if he and Haruka were followed by anyone at the convention, but he says he did not see anyone like that. That night, a frantic Haruka unexpectedly shows up at Yūto's house.

Haruka reveals that her father, Gentō, found out about her hobby and went on a rage, confiscating her anime goods and she leaves with her first issue of Innocent Smile. She hides in Yūto's house alongside Hazuki, while Mika prepares a 'secret weapon' to counter their father. Unfortunately, the next morning, Gentō arrives and assaults the Ayase house with his personal squad, the Hell Hounds. Haruka refuses to go home, and Yūto openly protests about the ostracization towards anime-otaku and disapproval towards Haruka's hobby. Eventually, Mika and Nanami arrives with their 'secret weapon': Haruka's mother Akiho, who verbally and mentally brings down Gentō and makes him leave after apologizing for his outburst.

Mika becomes angry when she realizes that the relationship between Yūto and her sister is not progressing as well as she expected, so she forces Yūto out on a date with her to teach him tips to get in the right mood with Haruka. During their date, they go to a café, and catch a movie before running into Shiina, which makes Mika jealous. Mika drags Yūto to a kimono shop and the two are outfitted with brand-new kimonos before heading to the summer festival and watching the fireworks with Haruka, Hazuki, and Nanami who find them. Once school starts again, Shiina volunteers to be one of the organizing members for her class' participation in the upcoming cultural festival, and Yūto gets dragged in to work with her.

Yūto's class decides to do a cosplay café for the school festival, for which Yūto asks Haruka to go to Akihabara with him to see examples of cosplay costumes. Unknown to Yūto, Haruka had previously made a promise to her father to meet his client, however she decides to go with Yūto to Akihabara instead. Gentō becomes furious when he finds out and goes and finds them, but Akiho comes just in time to save them again. Haruka makes cookies and goes to give them to Yūto, but is shocked when she finds Yūto on top of Shiina at school.

Haruka quickly leaves after seeing Yūto on top of Shiina, but when Yūto tries to explain the situation to her, Haruka says she understands, but ends up running back home. The next day during the school festival, Yūto finds Haruka to have apparently forgotten about yesterday, though Shiina is not so sure. Yūto confronts Haruka about yesterday again, but she tells him she does not want to hear what he has to say and runs off. Yūto runs into Hazuki as he is searching for Haruka, and she gives him so advice on how to move forward with Haruka. With Hazuki's help, Yūto finds Haruka behind the gym where he apologizes for yesterday and assures her that he will not leave her. Afterwards, the two dance by the tune of the music box Yūto gave her previously as Nanami, Mika, and Hazuki watch from the bushes.

Mika calls Yūto late at night to invite him to Haruka's birthday party on the evening of October 20. On the day of the celebration, Yūto goes to Akihabara to buy a gift and bumps into Nobunaga. After buying the gift, Yūto goes home and is fetched by Hazuki and Nanami to be taken to the party venue on an island far away together with Ruko and Yukari. On the island, Yūto meets up with Mika and Haruka. After meeting some of the guests, Yūto starts feeling insecure about his gift and social status.

The party has started and Yūto is dragged inside the party hall by Mika. While waiting for Yūto's turn to present his gift, he again bumps into one of the guests and his gift is ridiculed. Yūto becomes insecure and is about to leave the party hall when an old man, who happens to be Haruka’s grandfather, helps Yūto regain back his confidence. Yūto runs back to Haruka and presents his gift. After the party, Yūto is with Haruka in her room, and Yūto then realizes that he was the one who gave the copy of the first issue of Innocent Smile to Haruka when they were kids.

Yūto has lately been watching one of Haruka's favorite anime, Nocturne Girl's School Lacrosse Club. Yūto and Haruka along with several others are invited by Shiina to go to a hot spring in the mountains. Haruka is especially excited since this is her first trip with friends, due to having her hobby of watching anime being exposed in junior high school. Haruka's maids and her younger sister Mika also come along, as well as Yūto elder sister Ruko and Yūto's teacher Yukari Kamishiro. When everyone is out in town, Yūto finally manages to tell Haruka about an event close by to meet the voice actress of the lead character from Nocturne Girl's School Lacrosse Club. Nobunaga runs into Yūto and gives him two tickets for the event, as he did not know he had to buy them beforehand. Haruka enjoys the event and treasures it as a precious memory.

Yūto and Haruka begin making a dōjinshi together, though Haruka's skill in drawing is still lacking. Nobunaga asks Yūto to cover for him selling dōjinshi for one of his friends' dōjin circles at an upcoming event for Nocturne Girl's School Lacrosse Club. Yūto asks Haruka to accompany him, who is overjoyed at the prospect of helping out an already established circle. Yūto and Haruka continue their work on Haruka's illustration book of the Nocturne Girl's School Lacrosse Club lead character Haruna, though the day of the event Haruka's book is not selling. Nobunaga gives Yūto some advice, telling him that half the enjoyment is actually making the dōjinshi and Yūto realizes there are more important things that the book selling or not. Yūto goes back to Haruka and starts promoting Haruka's book, and eventually three people end up buying it.

After finding out that Haruka is working to get him a Christmas present, Yūto decides to apply for a well-paying job as a part-time butler. He gets the job, but he must unfortunately serve the selfish and demanding Tōka Tennōji, a girl one year his junior, whose previous part-time butlers quit after a day or less at her command. Yūto has his work cut out for him, but soon finds that there is more to Tōka's situation than he initially realized. Through kindness and hard work he manages to gain Tōka's favor, but a certain situation results in damages that cost him nearly all of his pay.

The Nogizaka family visits Yuuto's house for a Christmas party. However, the party is cut short when Yuuto faints, having worked himself to exhaustion to buy Haruka a Christmas present. When Yūto regains consciousness, Haruka declares that she will stay by his side in order to nurse him back to health, under the guidance of a very questionable guidebook prepared by Mika. To preserve the Christmas spirit in spite of Yūto's poor health, Haruka decorates his yard with Christmas lights, and presents him with a Christmas present. He in turn presents her with his present: a ring called "Clair de lune" which, at Haruka's request, he places on her ring finger. The two thus share another precious memory together.

Yuuto is invited to the annual encounter of maids and butlers due to his one week job at the Tennouji household. Yuuto is introduced to the rest of the Nogizaka family's maids and enjoys the party alongside Alice, until the arrival of Shute Sutherland, the same rich boy who caused him trouble during Haruka's birthday party, and because of it was ordered by his father to work as a butler for a while as a lesson in humility. After having his suit accidentally dirtied by Alice, Shute shouts at her and states how the butlers and maids at the party are inferior beings. However, Yuuto stands to protect Alice, and with Shute's father's approval, he and his lackeys are given the proper punishment by the members of the gathering. Yuuto is complimented by the other guests, and Alice mutters some words of thanks to him.

It is New Years Day and everyone has gone to visit the local shrine together. Although Haruka and Yūto were hoping to spend some time together, it is not long before Haruka's admirers, who are hostile to Yūto, whisk her away. Later, after both Haruka and Yūto receive encouraging fortunes (courtesy of Mika, Hazuki and Nanami—working as shrine miko), Haruka manages to get rid of those admirers. Haruka and Yūto bump into a mysterious girl, who is running away from someone. Later, Haruka takes Yūto to the cape where her parents shared their first kiss, so they can watch the sunrise together.

During the New Years break, Shiina expects something good from the fortune she received at the shrine, and coincidentally runs into Yūto on the street. Her hairpin gets knocked off into the river and Yūto goes in to retrieve it; as a thank you gift, Shiina prepares some cooked squid, but hurts her foot in the process. Mai and Ryouko, two of Shiina's friends, and Yūto come to pay her a visit, during which Yūto gives the three girls an unforgettable massage, a "punishment" for losing a game of old maid. Later on, Yūto and the others leave for the day, but Yūto comes back because he was worried about Shiina. Yūto helps her by preparing dinner, and the two spend the rest of the night having fun together. On the day Shiina returns to school from the holidays, she is cheerful, and gets giddier with joy when she meets Yūto, even with Haruka near him.

Yūto visits Mika's junior high school—an all-girls' school—upon her invitation. Mika introduces him to the rest of the girls in her class. He was surprised to know that Mika was a popular girl at school. She is a class president and a school idol, pretty much like her sister Haruka. After their meeting, Yūto decides to go and see Mika's stage play. After the stage play, both Yūto and Mika are accidentally locked up in the stage room. Luckily in the end, Mika's maids find them.

Haruka and Yūto are finally having some time for themselves. They go to the fair to have some fun together. There, Milan Himemiya's managers, Yayoi Kayahara and Nozomi Kobayakawa, get Yūto and Haruka to take a picture together. That night, they have a ride on the Ferris wheel and confirm their relationship, though not without the hijinks caused by a quite shaky Ferris wheel. Haruka's picture is taken to capture the moment. Yayoi and Nozomi then formally embarks on their real agenda for Haruka: grooming her into an idol.

Haruka agrees to attend the audition for Yayoi and Nozomi. Yūto waits as Haruka gets ready for the audition, and is told by Yayoi not to interfere. While waiting, Yūto once again bumps into the girl he met before at the shrine, who turns out to be the idol Milan Himemiya. Milan decides she wants Yūto as her manager since her own manager is currently in a different prefecture. Yūto and Milan go around together to photo shoots, voice acting and other things. After his work as a manager, Yūto overhears Yayoi and Nozomi while poring over Haruka's photographs. It becomes clear to him that the talent agency actually wants Haruka to become an idol—something Milan had tipped him of earlier.

Yūto has to make a tough decision of whether to stay with Haruka or leave her so she can become an idol. Yūto asks Milan to attend her concert on Valentine's Day. During the concert, Yūto, with some "on-stage prodding" by Milan, decides to leave so as to go to Haruka's audition. Shiina is worried about Yūto and Haruka's relationship. Yūto decides that he wants to stay with Haruka and it is finally revealed to the unaware Haruka how Yayoi had planned to make her into an idol. Yayoi and Nozomi try desperately to stop him, but Haruka's family and maids help to get the upper hand against them. The final blow comes when they are later forced out of their talent agency after Haruka's father buys it and all associated material from them in a hostile takeover. Later at the Nogizaka mansion, as Akiho and Gento watches Yayoi and Nozomi in some mud wrestling contest on TV, Haruka gives a Valentine's present to Yūto.

Yūto is invited to come with the Nogizakas to a ski resort in the mountains. He thinks it is just for them but he quickly finds out the entire class is coming on this trip. While the group enjoys all the hot spring resort has to offer, Shiina sees the trip as an opportunity to express her feelings to Yūto—but in an attempt to hug him, she ends up groping Gento, who was covered in sheets. An enraged Akiho catches them in a compromising position and gets the wrong idea, causing Gento to pass on the group's shrine visitation the next day. The next evening, a blizzard arrives and Haruka goes missing on the top of the mountain. When Yūto, equipped with an insulated polar bear suit, finds her, they both fall down a ridge and become stuck in a cabin. As she is wet and freezing, Haruka takes off her clothes and joins Yūto in his bear suit in just her underwear.