Sorata Kanda, a high school sophomore living in Sakurasou, the den of their academy's problem children, spends his days being dragged around by the strange residents, swearing he's going to escape Sakurasou one day.

At the end of the second semester of third year of high school, four students are prepared for graduation and feel the ending to their high school life. But that changes a little with the arrival of a transfer student.

Puberty Syndrome—a rumored, mysterious syndrome that only affects those in their puberty. For example, a bunny girl suddenly appeared in front of Sakuta Azusagawa. The bunny girl's real identity is Mai Sakurajima, a teenage celebrity who is currently an inactive high school senior. For some reason, her charming figure does not reflect in the eyes of others. In the course of revealing the mystery behind this phenomenon, Sakuta begins to explore his feelings towards Mai. Set in a city where the skies and seas shine, Sakuta unfolds the meaning behind his bizarre encounters on women with the said syndrome.

The anime follows a salaryman who has a chance meeting with a girl named Ai on the train. They begin to meet every Monday on the train, with the man serving as her bodyguard on the crowded commute while they chat.

The year is 2242. Kanata wants to be a Drifter and meets Noir, who is a dud Magus with no memories. However, because Noir excels in battle against the Enders, Kanata partners with her and discovers exactly what it takes to be a Drifter.