"Onii-chan Control" centers on the relationship between two siblings, Aki and her older brother Hiroshi. Aki, a high school student, harbors deep romantic feelings for Hiroshi, which she struggles to suppress due to societal norms and familial boundaries. Hiroshi, unaware of Aki's feelings, is a caring and protective older brother who often goes out of his way to support her. The story explores Aki's internal conflict as she navigates her emotions while trying to maintain a normal sibling dynamic.

The narrative delves into Aki's attempts to subtly influence Hiroshi's life, often under the guise of sibling concern. She intervenes in his relationships, sabotages potential romantic interests, and seeks to monopolize his attention. Hiroshi, oblivious to her true intentions, interprets her actions as typical sibling behavior. The tension escalates as Aki's feelings grow more intense, leading to moments of emotional vulnerability and moral dilemmas.

Secondary characters, such as Hiroshi's friends and Aki's classmates, add layers to the story by introducing external perspectives and complicating the siblings' dynamic. These characters often serve as catalysts for key plot developments, pushing Aki and Hiroshi to confront their feelings and the consequences of their actions.

The manga balances themes of unrequited love, familial bonds, and the ethical complexities of forbidden emotions. It portrays Aki's internal struggle with sensitivity, highlighting her desire for connection while acknowledging the societal taboos surrounding her feelings. The story progresses through a series of emotional highs and lows, culminating in moments of introspection and resolution for both characters.