"Kindred Spirits on the Roof" is a yuri manga series adapted from the visual novel of the same name by Liar-soft. The story is set in Yurigaoka Girls' Academy, a prestigious all-girls school, and revolves around the interactions between the living students and the spirits of two deceased girls who haunt the school's rooftop. These spirits, Yuna and Megumi, died decades ago and are unable to move on due to unresolved feelings about their relationship. They seek to experience love and intimacy vicariously by observing and encouraging romantic relationships among the current students.

The narrative begins when Toomi Yashiro, a reserved and studious student, discovers Yuna and Megumi on the rooftop. Initially startled, Yashiro becomes intrigued by their presence and agrees to help them fulfill their wish. Yashiro, along with her outgoing and mischievous friend Natsuki Iizuka, takes on the role of matchmaker, facilitating romantic connections between various students at the academy. The story explores multiple relationships, each with its own dynamics and challenges, as Yashiro and Iizuka navigate the complexities of love, friendship, and self-discovery.

Key characters include Yashiro, whose calm demeanor contrasts with Iizuka's playful nature, creating a balanced partnership in their matchmaking efforts. Yuna and Megumi, the spirits, provide a poignant backdrop to the story, their longing for connection serving as a catalyst for the events that unfold. Other students, such as the shy and artistic Ryouko Aiba, the confident and athletic Sachi Komine, and the enigmatic transfer student Sumika Chikage, each contribute to the evolving romantic entanglements. The series delves into themes of love, identity, and the enduring impact of relationships, both past and present, while maintaining a lighthearted and often humorous tone. The interplay between the living and the spirits adds a layer of supernatural intrigue, blending the everyday lives of the students with the ethereal presence of Yuna and Megumi.