Four boys named Haruka, Makoto, Nagisa and Rin all participated in a swimming tournament shortly before graduating elementary school and later parted ways. Years later, they reunite when Rin challenges Haruka to a race and wins. Not wanting to be defeated so easily, Haruka gathers Makoto and Nagisa and a new recruit named Rei to form the Iwatobi High School Swimming Club.
Tōko Fukami's family runs a glass-working business in a small seaside town. She hangs out with her four best friends at a cafe called "Kazemichi." During the summer break of their senior year in high school, they meet a transfer student named Kakeru Okikura, who claims that a voice from the future talks to him, and that it's led him to Tōko. His arrival sets off a series of events that will make their final summer together one full of hope and heartache.
A girl named Mitsuki Kanzaki lives with her step-brother Yuya after her mother remarries. One day, Mitsuki is possessed by the self-proclaimed spirit of a young girl, Hiyori Kotobuki. Hiyori (in Mitsuki's body) must fall in love with Yuya to move toward the "Gates of Heaven."
Yōto Yokodera is a perverted schoolboy who is unable to express his true feelings freely. After hearing about the wish-granting Stony Cat, he decides to try and make an offering to lose his facade, only to meet Tsukiko who wishes instead to be more discreet with her feelings to become more adultlike. Who'd have thought the rumors of the wish-granting Stony Cat turns out to be true; transferring the facade that Yōto wishes to lose into a classmate who needs it more and making it difficult for Tsukiko to show even the slightest of emotions on her face. Being on the same boat, they both search for ways to remedy the situation.