In the winter of 1945, Sakura the elephant gave birth to a baby elephant at Tokyo Fujimi Zoo under the watchful eye of the zookeeper Shota Tanabe. Around the same time, Shota's wife, Setsuko, also gave birth to a son. Hanako, the baby elephant, grows up while deepening her bonds with elementary school students who love zoos. However, as Japan enters the Pacific War, the military orders the animals in the zoos of five major cities to be killed.

Sen Rikyu is a ceremonial tea master who advises warlord Hideyoshi in sixteenth-century feudal Japan. His daughter, the beautiful Lady Ogin, has an unrequited love for Lord Ukon, who has angered Hideyoshi by becoming a Christian convert. Ogin's father Rikyu also displeases Hideyoshi by opposing the warlord's plan to invade China and Korea. When the animalistic Hideyoshi is rejected by Ogin, he threatens her and her father with arrest and worse.