High schoolers Mio Miyamasu and Arata Kishimo are childhood friends. Mio harbors feelings for Arata, but she lacks the courage to express them. Even when her friend Madoka asks if she is in love with Arata, Mio reluctantly declines and encourages her friend to pursue her own feelings for him instead. Later, while Mio and Arata visit a fortune-teller, the boy notices a strange phenomenon and tries to drag Mio out of the shop—much to her annoyance. As Mio begins to question her relationship with Arata, an argument erupts between them. That night, feeling guilty for what had occurred, Mio ventures into the rain to apologize to Arata and make her feelings clear. However, an accident along the way turns Mio's world upside down.

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Kimi wa Kanata was originally intended to be a short film, but it was turned into a feature film after many script revisions.