Mitsuha Miyamizu is a high school girl living in the rural town of Itomori near Hida. Bored of the town, she wishes to be a Tokyo boy in her next life. She inexplicably begins to switch bodies intermittently with Taki Tachibana, a high school boy in Tokyo, waking up as the other person and having to live through their activities and social interactions for the day. The two initially believe these experiences to be vivid dreams, but eventually realize they can communicate with each other by leaving messages on paper, phones and sometimes on each other’s skin. Mitsuha (in Taki’s body) sets Taki up on a date with his coworker Miki Okudera, while Taki (in Mitsuha’s body) causes Mitsuha to become popular at school. One day, Taki (in Mitsuha’s body) accompanies Mitsuha’s grandmother Hitoha and her sister Yotsuha to leave the ritual alcohol kuchikamizake, made by the sisters, as an offering at the Shinto shrine located on a mountaintop outside the town. It is believed to represent the body of the village guardian god ruling over human connections and time. Taki reads a note from Mitsuha about the comet Tiamat, expected to pass nearest to Earth on the day of the autumn festival. The next day, Taki wakes up in his body and goes on a date with Miki, who tells him she enjoyed the date but also that she can tell that he is preoccupied with thoughts of someone else. Taki attempts to call Mitsuha on the phone, but cannot reach her and finds the body-switching has ended.
Taki, Miki, and their friend Tsukasa travel to Gifu by train on a trip to Hida, though Taki does not know the name of the town, instead relying on sketches he has made of the surrounding landscape from memory. A restaurant owner in Hida recognizes the town in the sketch as Itomori, being originally from there. He takes Taki and his friends to the ruins of the town, which has been destroyed and where five hundred residents were killed when the comet Tiamat unexpectedly fragmented three years earlier. While gazing over the impact crater in disbelief, Taki observes Mitsuha’s messages disappear from his phone and his memories of her begin to gradually fade. Taki finds Mitsuha’s name in the record of fatalities, and he wonders if the body-switching was just a dream. While Miki and Tsukasa return to Tokyo, Taki journeys to the shrine, hoping to reconnect with Mitsuha and warn her about the comet. In the shrine, Taki drinks Mitsuha’s kuchikamizake then lapses into a vision, where he glimpses Mitsuha’s past. He also recalls that he had already encountered Mitsuha on a train three years earlier when she came to Tokyo in her own timeframe to find him, though Taki did not recognize her as the body-switching was yet to occur in his timeframe. Before leaving the train in embarrassment, Mitsuha had handed him her hair ribbon, which he has since worn on his wrist as a good-luck charm.