Childhood friends Shunta Shii and Tamaki Yuminaga have grown up together, their bond seemingly unbreakable despite the single year that separates them in age and school grade level. Their relationship takes a dramatic turn when Shunta discovers Tamaki crying one day, an event that awakens unexpected romantic and sexual feelings within him. Shunta immediately views these emotions as monstrous and impure, setting the stage for an internal conflict that drives much of the storys tension.

The narrative follows these two boys as they navigate high school while their friendship undergoes a profound transformation. Shunta struggles with his growing attraction, feeling increasingly like a scared rabbit afraid to reveal his true feelings. The story gains complexity when Tamaki confides in Shunta about a recent breakup, revealing that he does not like girls. However, Tamaki also expresses doubt about whether pursuing relationships with boys is a feasible alternative for him, leaving Shunta wondering if he can change his best friends mind about the limitless possibilities of love.

The setting primarily revolves around their school environment and the track-and-field club, where both boys participate. Tamaki, a second-year student, achieves a personal best time of 11.92 seconds in his sprint event, while first-year Shunta records 13.78 seconds. The athletic setting provides a backdrop for their interactions and the natural progression of their relationship as they support each other during training and competitions.

The narrative arcs delve deeply into the psychological aspects of both characters. Shunta is depicted as taciturn and sexually precocious, actively seeking to move his relationship with Tamaki forward. At one point, his internal conflict becomes so overwhelming that he cuts off contact with Tamaki for an entire year and even takes a college-aged lover while still in middle school. Meanwhile, Tamakis reluctance toward physical intimacy stems from a troubled family background, having grown up in an unhealthy environment with his mother, a single parent who worked as an escort and exposed him to inappropriate situations during his childhood.

The manga explores themes of self-acceptance, the fear of rejection, and the struggle between maintaining a cherished friendship and pursuing romantic love. The title Forest of the Rabbits reflects Shuntas perception of himself as timid and fearful, constantly second-guessing whether to reveal his true feelings to the person he cares about most.