"Wagamama High Spec" centers around the life of Kusunoki Kousei, a high school student who secretly works as a manga artist under the pen name "Kujou Aoi." His double life becomes complicated when his classmate, Saegusa Koharu, discovers his secret. Koharu, who is the student council president, offers to keep his identity hidden in exchange for his help with the student council. Kousei reluctantly agrees, leading to a series of comedic and lighthearted interactions.

The narrative expands as other characters become involved in Kousei's life. Murasaki Kokoro, a first-year student and Kousei's younger stepsister, is a talented violinist who harbors feelings for him. Narumi Kana, a cheerful and energetic classmate, is a fan of Kousei's manga and eventually learns about his secret. Lastly, Tachibana Mihiro, the school's strict disciplinary committee chair, also becomes entangled in the group's activities, adding to the dynamic.

The story explores themes of friendship, personal growth, and the challenges of balancing multiple responsibilities. Each character brings their own quirks and struggles, contributing to the series' comedic and slice-of-life tone. The interactions between Kousei and the other characters often revolve around their attempts to navigate school life while dealing with the complications arising from his secret identity. The series maintains a light-hearted atmosphere, focusing on character relationships and everyday school events rather than high-stakes drama.