Puberty syndrome – Abnormal experiences rumored on the internet to be caused by sensitivity and instability during adolescence. This year, Sakuta Azusagawa, a second-year student at a high school near Enoshima, meets several girls that are experiencing this “puberty syndrome.” For instance, he meets a wild bunny girl in the library. She turns out to be an actress on hiatus, Mai Sakurajima, who is also his senior at the school. For some reason, no one else can see this enchanting girl. How did she become invisible…? As Sakuta searches for answers to help Mai, they spend more time together, and he eventually learns of her hidden feelings… This is an unusual story that takes place in a town of bright skies and glistening seas, where Sakuta encounters various intriguing girls.

While looking for the cause of Mai's Adolescence Syndrome, Sakuta ends up scheduling a date with Mai. On the day they promised, Sakuta tries to help out a lost little girl on his way towards Fujisawa Station. But, he is misunderstood to be a perverted maniac by another girl, and because of that, he ends up arriving late to his appointed time to meet Mai. He somehow gains Mai's forgiveness and they proceed with their date, but Mai changes their destination, and takes Sakuta to Shichirigahama Beach...

Even after leaving Fujisawa for Ogaki, not one person remembered anything about Mai Sakurajima. Sakuta and Mai return to school together, but even there they hear from Sakuta's friend Rio Futaba that nobody at school outside of her has any recollection about Mai. At the same time, Sakuta hears of a theory that losing memories concerning Mai is based on a certain action taken, and struggles so that he doesn't lose his memories of her. And seeing Sakuta act as such, Mai makes a certain decision of her own as well...

Soon after Mai's "puberty syndrome" is resolved, Sakuta encounters another strange phenomenon without respite. Day after day, it is the same day for Sakuta and there is no tomorrow. When he consults Rio, she raises the possibility of "Laplace’s demon" -- that someone may be repeating and redoing a day.

Because of the misunderstanding that she was dating Sakuta, Tomoe is able to resolve the agonizing situation of being asked out by the guy her friend is in love with. She pleads with Sakuta to continue acting like they are dating. Despite feeling indebted to Mai, Sakuta could not leave Tomoe alone as she was fearing that she would lose her presence within her class. So, he reluctantly agrees to play the role of Tomoe's fake boyfriend for a while.

It is now the last day of the first term, the promised day when pretending to be dating Tomoe ends. It seems as though everything has finally been resolved, but…

After agreeing to harbor an abandoned cat, Sakuta finds himself welcoming a look-alike to his old school crush into his home. This does not sit very well with Mai, who is trying her best to be with her boyfriend amidst a demanding work schedule. Meanwhile, something appears to be up with Futaba...

Upon inducing a case of "Puberty Syndrome" where two copies of herself exists, Rio ends up staying at Sakuta's house for the time being. Meanwhile, "the other Rio" has been busy posting various unexpected photos on social media. After being informed about these activities by his classmate, Saki Kamisato, Sakuta decides to have a chat with "the other Rio." As he learns more about each of the Rio-s in hopes of discovering the reason for "the other Rio’s" actions and possibly a cure for her "Puberty Syndrome," Sakuta begins to realize the troubles each of them carries...

Sakuta had been unable to see Mai, who was not only busy with work but had an order from her agency forbidding her from going on dates. The second term finally begins, and Sakuta is eagerly looking forward to seeing Mai again at school. But upon seeing Mai in front of his house, she greets him with a shocking, "Who the heck are you?" Upon confirming what the circumstances are, it comes into light that Mai and her little sister Nodoka Toyohama have swapped bodies. Until this new Adolescence Syndrome is resolved, Mai will be living as Nodoka, and Nodoka will be living as Mai...

Unable to deal with a commercial filming well as the actress Mai Sakurajima, Nodoka gradually starts to feel a strong sense of inferiority. As their body-swapped lives continues on, the day arrives where Mai must perform in Nodoka's pop idol group "Sweet Bullet". Sakuta and Nodoka attend the concert as they were given tickets...

With Nodoka's Puberty Syndrome resolved, Sakuta's expectations to spend sweeter times with Mai is growing. But then, a scandal is reported by the media about Mai Sakurajima having a new boyfriend. In the press conference for a movie she had a role in, Mai gives a sincere explanation. Seeing that, Kaede decides to set goals for the rest of the year, wanting to do her best for Sakuta's sake as well. One of the goals she writes down is to go back to school...

Sakuta unveils to Mai and Nodoka the details of his family's past, and the trauma that Kaede underwent. Meanwhile, Kaede continues her re-integration into society, but as more hurdles appear, Sakuta worries for his sister's well-being.

With Sakuta's help, Kaede is able to go to school at night. She is now enthusiastic about heading to school during the day. However, on the following day, the original Kaede's memory suddenly returns, eradicating all memories of the Kaede that had spent the last two years together with Sakuta. A certain person appears before Sakuta, who is overwhelmed with grief because Kaede was no longer around.