At school, Mio Miyamasu and her classmate and childhood friend Arata Kishimo discuss the boundary between sky and space, with Arata suggesting it is called "over the sky". After her markup exam, Mio is approached by her best friend Madoka and learns that she also likes Arata, causing uneasiness since she has trouble admitting her feelings. Arata begins to see several white orbs while visiting a fortune-telling shop with Mio. The two argue afterward, with Mio leaving Arata behind after questioning their relationship. Later night, a heartbroken Mio decides to tell her true feelings for Arata, but she gets involved in a traffic accident.

The next day, Mio tries to approach Arata but seems unnoticed by him. As they ride home, Mio is transported to a different world called "World Border" and meets her favorite character Gimon. As Gimon guides Mio to a new world where she will forget everything, they are stopped by a kimono-wearing girl who introduces herself as Kiku-chan. Kiku-chan explains that she accidentally arrived in World Border due to an out-of-body experience, and needs to be returned to the human realm using a train ticket and the "desire" to return. Mio contacts Arata, who mysteriously answers it while in a hospital to visit Mio's unconscious body. Mio, Gimon, and Kiku-chan arrive at Forgotten Things Counter, but Mio has trouble telling the lost-and-found officer her memories with Arata so they visit the goddess, Mrs. Mori, for help. Following the mysterious call from Mio, Arata returns to the fortune-teller for help, but his soul suddenly leaves his body to arrive at the World Border.

Despite successfully obtaining a ticket from the lost-and-found officer, the World Border's guardian Mogari prevents Mio from returning to the human realm. With the help of Gimon, Kiku-chan, and Arata, Mio arrives back to the human realm but is unable to reunite with her body. Arata brings Mio's unconscious body to the cliff where he has a great memory with her and hopes for her soul to return. Mio, accepting her fate, firmly resolves to return to the human realm, finally remembering her "desire" to tell Arata her love for him. She successfully returns to the human realm and reunites with Arata.