"Natsuiro Kiseki" centers around four childhood friends—Natsumi, Saki, Yuka, and Rinko—who discover that a large rock in their neighborhood park, known as the "Wishing Rock," has the power to grant wishes. The series explores their summer adventures as they navigate the complexities of friendship, personal growth, and the bittersweet realities of impending change. Each girl harbors her own desires and struggles, which are brought to light through their interactions with the rock and each other.

Natsumi, the energetic and impulsive leader of the group, often pushes her friends to take risks and embrace spontaneity. Saki, calm and level-headed, serves as a grounding force, though she grapples with her own insecurities about the future. Yuka, cheerful and optimistic, hides a deeper longing for connection, while Rinko, shy and reserved, struggles to express her feelings and assert herself. The rock's magic becomes a catalyst for their individual and collective journeys, as their wishes lead to unexpected consequences and revelations.

The narrative unfolds episodically, with each wish revealing more about the characters' inner lives and relationships. Themes of nostalgia, the passage of time, and the inevitability of change are woven throughout the story. The girls' bond is tested as they confront the challenges of growing up, including the possibility of separation as they approach the end of their middle school years. The series balances moments of lighthearted humor and heartfelt emotion, capturing the essence of a fleeting summer and the enduring strength of friendship.