Kun, a spirited 4-year-old boy, is the cherished son of an executive mother and an architect father. They reside in a unique stepped house located in Kanazawa-ku, Yokohama, designed by Kun's father around a grand tree. Kun enjoys delightful days filled with play alongside his pet dog, Yukko, and immersing himself in his colorful toy train sets. However, the arrival of his baby sister, Mirai, whose name translates to "future," brings about a shift in dynamics. Initially, Kun welcomes her, but as time progresses, jealousy takes root as all the parental attention shifts to the newborn, leaving him to act out, particularly as his father, now working remotely, becomes preoccupied with his job.
One day, after a particular outburst, Kun retreats to the garden and encounters a peculiar man who claims to be the “prince” of the house. This man lamenting about losing everyone's focus upon Kun's arrival soon reveals himself to be none other than Yukko transformed into a human. Kun, intrigued and playful, finds a tail resembling Yukko's on this stranger. Upon placing it on himself, a magical transformation occurs, turning him into a dog.
During Hinamatsuri (Girls Day), the family partakes in a special tradition by displaying traditional dolls to wish for Mirai’s happiness. However, as days pass and the dolls remain up post-holiday due to his father's oversight, Kun's frustration boils over again, leading him back to the garden. This time, he encounters a teenage girl who identifies herself as Mirai from the future. Kun recognizes her by a distinct birthmark on her hand. She reveals that her presence in the past is urgent; for every day the dolls linger, a year is added before she can wed. With the help of Future Mirai and the anthropomorphized Yukko, Kun assists in putting the dolls away.
In the garden once more, Kun's journey transcends time as he is whisked back to snapshots of the past. He encounters a young version of his mother, who is grappling with her own childhood frustrations. Recognizing her from family photos, Kun sympathizes with her struggles, especially when he witnesses her messages to her grandmother regarding a desired pet cat. Although Kun returns to his own time with newfound understanding of his mother, his complaints persist.
One day, Kun leaves a note asking for a bicycle and is overjoyed when he receives one with training wheels. However, yearning to ride like the older kids, he struggles to maintain balance. His quest for mastery takes him back to the magical garden, catapulting him into a workshop in rural Japan, where he meets a young man with a wounded leg—his great-grandfather. This encounter culminates in a thrilling ride that instills confidence and knowledge in Kun, allowing him to eventually ride his bike independently. The revelation of his great-grandfather's identity after returning to the present adds another layer to Kun's understanding of family history.
As the family plans a day trip, Kun's irritation re-emerges regarding his clothing. During this escapade into the garden, he discovers a train station, where an older young man warns him against boarding a train. Disregarding the advice, Kun finds himself at Tokyo Station, overwhelmed and lost. A kind attendant offers assistance, but Kun realizes he cannot even recall his parents' names. The atmosphere intensifies when the attendant mentions a bullet train leading to “Lonely Land,” which symbolizes despair; however, when he spots baby Mirai ready to board the train, he instinctively rescues her, finally acknowledging his role as her older brother.
In a breathtaking turn, Future Mirai arrives to transport Kun home, soaring through the air and landing in the family tree. Here, he witnesses moments from their past—his father’s childhood struggles, Yukko's choice to become a pet, his mother's lost fascination with cats, and the impact of World War II on his great-grandfather. He is then confronted with glimpses of the future, where he recognizes the older man at the station as a vision of his future self.
Back in the present, having gained profound insights and empathy, Kun is now ready to join his family on their adventure, embracing the bonds that connect them all.
