Forgetful and good-natured Run Momoki has been best friends with Tooru Ichii since childhood. Despite Run being one year older, her carefree attitude and popularity with the boys is a constant headache for the overprotective Tooru. To complicate matters further, when Tooru applies to the same high school as Run, she finds out that their little circle of two has grown into a quartet. Their new acquaintances—Nagisa Tennouji and Yuuko Nishi—are classmates of Run and, in Tooru's eyes, the two must prove they are trustworthy. As a new high school year begins, the girls balance their friendship with the exhilarating opportunities of school life.

What do an alien, former ninja, weak telepath, and boy pretending to be a girl have in common? They are all classmates at Kashihara Girls' Academy, and they hide their true identities from the world. Rikka, Chiyo, Sekine, and Tsubasa seem like the best of friends, but they each harbor a monumental secret that they cannot reveal, no matter what. In order to continue masquerading as normal middle school girls, each of them must invent creative ways to conceal their true selves. But that is easier said than done, as the four students end up entangled in numerous shenanigans along the way.

Tensho School is located in the 7th Ward of Thrive Central, where emphasis is put on extracurricular activities and all clubs participate in an annual fall singing contest. Having to delay the start of his school year due to his older sister's hospitalization, transfer student Saku Otonomiya finds himself struggling to adapt to his hectic new life. Balancing his part-time job and caring for his sister, he finds it difficult to make time to join a school club. In preparation for the upcoming singing contest, the school's singing club wishes to use Sousuke Kagura's song Cloudy Days, but Kagura is reluctant to grant his permission. The song requires someone with a three-octave range to sing it and he believes that only a VOCALOID can meet the standards. He allows for the club to use his song on the condition that they can find someone who possesses that vocal range to properly sing it. While racking his brain over the composition of his next song, Kagura stumbles upon Otonomiya singing Cloudy Days perfectly. He invites Otonomiya to form a unit with him for the competition. At the same time, the singing club tries to goad him into joining so they can use Kagura's song. As the contest inches closer, Otonomiya must overcome his uncertainty and decide who to team up with.

Somewhere in the school at noon, one might hear the sound of two girls playing table tennis together as they wait for time to pass by. As if by fate, two students—Sakura Adachi and Hougetsu Shimamura—stumble upon each other on the second floor of the school gymnasium. As they gradually foster a budding friendship, their feelings for one another only become more ambiguous. Growing closer by the day, the two must learn to navigate their contrasting personalities as well as determine the depth of their affection for each other. The nature of this relationship gradually shifts when one of them starts to develop feelings beyond the boundaries of a platonic relationship. Even so, Adachi and Shimamura must realize if forming a bond stronger than friendship will bring them closer or tear them apart.