"Kimi dake ni Motetainda" centers on Kazuki Yoshikawa, a high school student who harbors feelings for his classmate, Rino Endo. Despite his efforts to confess his love, Kazuki struggles to find the right moment and courage. His life takes an unexpected turn when he discovers a mysterious app on his phone that allows him to see the romantic compatibility between himself and others as a percentage. Intrigued, Kazuki begins using the app to gauge his chances with Rino, only to find that their compatibility is surprisingly low.

As Kazuki navigates this revelation, he encounters other girls whose compatibility percentages with him are significantly higher. Among them are Natsuki Enomoto, a cheerful and outgoing classmate; Ayaka Tachibana, a reserved and studious girl; and Misa Kuroki, a childhood friend with a playful demeanor. Each girl presents a unique dynamic, and Kazuki finds himself drawn into various romantic situations as he tries to understand his feelings and the app's implications.

The narrative explores themes of love, self-discovery, and the complexities of relationships. Kazuki's journey is marked by moments of introspection as he questions whether the app's predictions should dictate his actions or if genuine emotions hold more weight. The series balances lighthearted comedic moments with heartfelt scenes, creating a blend of romance and slice-of-life elements.

Throughout the story, Kazuki's interactions with Rino, Natsuki, Ayaka, and Misa reveal different facets of his personality and challenge his preconceptions about love. The app serves as both a catalyst for his romantic endeavors and a source of conflict, as he grapples with the ethical and emotional implications of relying on it. The series ultimately delves into the idea that love cannot be quantified and that true connections are built on mutual understanding and effort rather than predetermined compatibility.