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.

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...

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.

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...

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...

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...

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.