Hiroki Fujisawa and Takuya Shirakawa harbor admiration for two things in their life: their classmate Sayuri Sawatari and the vast Ezo Tower that stands boundlessly across the Tsugaru Strait. Fascinated by the limitless structure beyond their reach, Hiroki and Takuya begin constructing an aeroplane from a fallen drone they discovered—naming it the Bella Ciela—to fulfill their dream of one day reaching the sky-scraping top of the tower. Later joined by the girl they love, Hiroki and Takuya promise Sayuri to fly with her to the seemingly otherworldly top together. However, Japan has suffered a North-South partitioning that has fueled conflict near the base of the tower, which marks the border between the America-controlled Southern islands and the Northern lands occupied by the Soviet Union. Further along, Sayuri suddenly disappears, and Hiroki and Takuya never see her again. Unbeknownst to them, she fell victim to a sleeping disorder that left her comatose for the past three years. Although Hiroki and Takuya later learn about Sayuri's condition, they also discover that the girl's unconscious state is oddly linked to the same tower the trio had promised to conquer together.

One Christmas Eve, Hana, Gin, and Miyuki are rummaging for presents through heaps of garbage when they chance upon an abandoned baby in the cold winter night. Appalled at the pitiful sight, Hana's maternal instincts kick in and she insists on finding the baby's biological mother to demand an explanation. Naming the baby Kiyoko—meaning pure child—they begin their search using the possible clues left alongside her: a mysterious key and a single note. However, their plans are soon thrown into disarray as they get caught up in a series of unprecedented events. Tokyo Godfathers follows the journey of the trio as they stick together through thick and thin, hoping to deliver Kiyoko to her true home, and find their very own Christmas miracle.

In 1950s Japan, Tatsuo Kusakabe relocates himself and his two daughters, Satsuki and Mei, to the countryside to be closer to their mother, who is hospitalized due to long-term illness. As the girls grow acquainted with rural life, Mei encounters a small, bunny-like creature in the yard one day. Chasing it into the forest, she finds Totoro—a giant, mystical forest spirit whom she soon befriends. Before long, Satsuki too meets Totoro, and the two girls suddenly find their lives filled with magical adventures in nature and fantastical creatures of the woods.

One summer, Norimichi Shimada and his friends want to know if fireworks look round or flat from the side. They forge a plan to find the answer at Moshimo Festival's fireworks display. However, Norimichi finds himself conflicted when his classmate, Nazuna Oikawa, plans to run away from home and wants Norimichi to join her. When things go awry in their attempt to escape, a strange orb in Nazuna's possession gives them another chance at staying together.