After a slow but eventful summer vacation, Shuchiin Academy's second term is now starting in full force. As August transitions into September, Miyuki Shirogane's birthday looms ever closer, leaving Kaguya Shinomiya in a serious predicament as to how to celebrate it. Furthermore, the tenure of the school's 67th student council is coming to an end. Due to the council members being in different classes, the only time Kaguya and Miyuki have to be together will soon disappear, putting all of their cunning plans at risk. A long and difficult election that will decide the fate of the new student council awaits, as multiple challengers fight for the coveted title of president.

The elite members of Shuchiin Academy's student council continue their competitive day-to-day antics. Council president Miyuki Shirogane clashes daily against vice-president Kaguya Shinomiya, each fighting tooth and nail to trick the other into confessing their romantic love. Kaguya struggles within the strict confines of her wealthy, uptight family, rebelling against her cold default demeanor as she warms to Shirogane and the rest of her friends. Meanwhile, council treasurer Yuu Ishigami suffers under the weight of his hopeless crush on Tsubame Koyasu, a popular upperclassman who helps to instill a new confidence in him. Miko Iino, the newest student council member, grows closer to the rule-breaking Ishigami while striving to overcome her own authoritarian moral code. As love further blooms at Shuchiin Academy, the student council officers drag their outsider friends into increasingly comedic conflicts.

Having a friend that knows you inside out should be a good thing, but in Nishikata's case, the opposite is true. His classmate Takagi loves to tease him on a daily basis, and she uses her extensive knowledge of his behavior to predict exactly how he will react to her teasing, making it nearly impossible for Nishikata to ever make a successful comeback. Despite this, Nishikata vows to someday give Takagi a taste of her own medicine by making her blush out of embarrassment from his teasing.

With the initiation of the Patrian civil war came the creation of half-beast, half-human soldiers—a development of the outnumbered Northerners in a desperate attempt to counter the overwhelming Southern forces. Able to quickly dominate battlefields and achieve victory with ease, the soldiers' godlike abilities earned them the name Incarnates. However, as the war raged on, the Incarnates encountered a problem involving the beasts inside them that they were unable to rectify by ordinary means. Once the war was over, mysteries and accounts of the Incarnates submitting to the misfortune of their war days surfaced. Aware of the horrors they faced during the war, Special Sergeant Major and former captain of the Incarnates Hank Henriette becomes a Beast Hunter—those who take the lives of Incarnates who have succumbed to the issues they experienced on the battlefields. After witnessing her father, a former Incarnate soldier, meet his end at the hands of one such Beast Hunter, Nancy Schaal Bancroft resolves to hunt the man who took her father's life. However, Nancy's eye-opening encounter with the Beast Hunter influences her to instead seek the reason behind her father's death and the Incarnates' problematic existence in society.