"Homeroom Affairs" centers on the intricate dynamics within a high school classroom, where personal relationships and hidden tensions shape the narrative. The story unfolds in a prestigious academy, focusing on Class 3-A, a group of students whose lives intertwine through academic pressures, romantic entanglements, and unresolved conflicts. The protagonist, Haruto Saito, is a reserved yet observant student who becomes an unintentional mediator among his peers. His quiet demeanor contrasts with the vibrant personalities around him, including the charismatic class representative, Aoi Takahashi, and the enigmatic transfer student, Rika Nakamura, whose arrival disrupts the class's fragile equilibrium.

The plot delves into the complexities of adolescence, exploring themes of friendship, rivalry, and self-discovery. Haruto's interactions with his classmates reveal layers of unspoken emotions, as secrets and misunderstandings come to light. Aoi, admired for her leadership and confidence, struggles with her own insecurities, while Rika's mysterious past creates tension and curiosity among her peers. The narrative weaves through various subplots, including a love triangle involving Haruto, Aoi, and Rika, as well as the competitive academic environment that fuels both camaraderie and conflict.

Secondary characters, such as the mischievous Kenta Mori and the studious Yuki Tanaka, add depth to the story, highlighting the diverse personalities within the class. The series balances lighthearted moments with dramatic turns, as the students navigate their final year of high school. Key events, such as the school festival and midterm exams, serve as catalysts for character development and emotional revelations. The story culminates in a poignant graduation ceremony, where the bonds forged throughout the year are tested and reaffirmed, leaving a lasting impact on the characters' lives.