The story returns to Hekiyou Private Academy in Hokkaido, where the student council is selected through a pure popularity contest, resulting in a group of the school's most attractive and talented girls. The sole male member, Ken Sugisaki, earned his place not through popularity but by scoring first on the entrance exams, a feat he accomplished with the explicit goal of creating his ideal harem. As the second season, Level 2, begins, the council room looks different, some voice actors have changed, and a new, more serious undercurrent runs beneath the usual jokes. The ever-present threat of graduation now looms closer for the youthful president Kurimu Sakurano and the super-sadistic secretary Chizuru Akaba. With the energetic vice-president Minatsu Shiina and the gentle otaku treasurer Mafuyu Shiina also facing an uncertain future after their school transfers, the days of the current student council are numbered.

As Ken continues his outrageous yet oddly dedicated pursuit of the four girls, the season deepens its focus on the past and the future. An episode zero flashback reveals the lonely and directionless first year of high school that drove Ken to study obsessively, showing his rivalry with the sharp-tongued genius Runa Minase and the origins of his quest to reach the student council. The present-day narrative introduces new characters from his past who threaten to disrupt the fragile balance of the council. His innocent and adoring half-sister, Ringo Sugisaki, arrives and immediately sparks jealousy among the other members, while his cheerful childhood friend and former girlfriend, Asuka Matsubara, reappears with the intention of winning him back and ending his harem ambitions.

Unlike the first season's rapid-fire parody comedy, Level 2 shifts its tone to include more romantic development and emotional weight, giving individual focus episodes to members like the tomboyish Minatsu as she struggles to express her softening feelings for Ken. The narrative builds toward the impending separation, forcing each character to confront their true feelings. Ken, who has always declared his love for the student council itself, finds his real intentions put to the test. Throughout the season, the four girls each find moments to express their appreciation and love for him, moving beyond the slapstick abuse of the past to a more genuine mutual affection. The final arc revolves around Ken’s attempt to ensure the group stays together and to properly convey his feelings before the graduation ceremony ends their time in the student council room, culminating in a resolution where the bonds they have formed prove stronger than any school transfer or graduation date.