The film opens with Ai, an 11-year old young girl, moving into the Animal Village during the summer. After being put to work by Tom Nook to deliver goods, Ai befriends four of the village's residents: Bouquet, Sally, Albert, and Yū, participating in several activities. Ai begins to find a series of anonymous messages in bottles that state that a miracle will occur during the upcoming Winter Festival if pine trees are planted in specific points of the village. Ai complies with the messages and begins planting the trees, half-believing that the messages may have been placed by aliens.
During autumn, Bouquet scolds Ai for not attending Sally's farewell party, which comes as a big surprise. Ai becomes heartbroken, learning that Margie has moved away to embark on a career in fashion design. Ai ends up at the museum café, and ends up crying when K.K. Bossa plays, as the song reminds her of Sally. Bianca scolds Ai, and tells her that she should be happy as a friend for Sally. Ai then responds by saying that she is happy, but she is instead sad that Sally never told her anything, and leaves the café. Sally sends a letter of apology to Ai, explaining that a goodbye would have been too upsetting, and encourages her to embark on her own personal journey. Bouquet apologizes to Ai for her harsh reaction.
Winter comes, and all the pine trees that Ai has planted have fully grown and are decorated with Christmas lights. A spaceship crash-lands in the middle of the forest, and Johnny, a seagull, emerges. Johnny, who had planted the bottles in order to make an entrance dressed as an alien, asks the villagers to help locate some of the pieces that broke off his ship during the descent. Ai, Bouquet, Yū, and Albert head towards a cave, where Yū claims to have seen one of the pieces fall. The entrance, though, is blocked up by a large boulder from a recent event. Though the team tries to move the boulder, it eventually turns out it is too heavy for them to move. Sally then appears and helps unseal the cave.
The five retrieve the missing piece and return to Johnny, who they discover had already obtained them all. The missing piece turns out to be an injured UFO, one of a larger group that was attracted to the village due to the pattern formed by Ai's lit-up pine trees. The injured UFO reunites with its group, and as they depart, create a constellation in the night sky resembling Ai. Ai then wins the Winter Festival contest for the best decoration, leaving her feeling for the first time as a true member of the village.