Wataru Murakami is a Japanese boy residing in Kenya during World War II in 1941. His father, Daisuke Murakami, works as a nuclear researcher and textile trader within the British colony. When war erupts between Japan and the Allies, Wataru and his father flee into the wilderness to evade arrest by British authorities. A rhino attack tears them apart, leaving Wataru stranded alone in the Kenyan wilds.

Initially terrified, Wataru displays early resilience by aiding an ailing Maasai chief named Zega. He fetches water and medicinal herbs for the chief, saving his life. In gratitude, Zega abandons his tribal duties to accompany Wataru on his quest to find his father, marking the start of Wataru's transformation.

Over several years (cited variably as two to four), Wataru evolves from a vulnerable child into a proficient survivalist under Zega's tutelage. He masters spears and swords, learns elephant riding, and adapts to the African wilderness's perils. Montages occasionally depict his physical development and acquired skills.

During their journey, Wataru and Zega encounter Kate, a blonde-haired girl presented as a deity by a manipulative tribal leader. They rescue her, and she joins their quest. This trio confronts numerous threats, including hostile tribes, fantastical creatures like elephant-sized toads and giant snakes, and Nazis developing atomic weapons. Wataru frequently draws courage from his Japanese heritage, with others commenting on his perceived strength due to his ethnicity.

Wataru's journey culminates in extraordinary events: a nuclear explosion triggered by German scientists opens a time portal to the Mesozoic era. Surviving dinosaur encounters with help from a giant serpent named Dahna, he returns to his own time. He is ultimately reunited with his father and departs Kenya by train alongside him and Kate as the war ends.