Wataru Murakami is an 11-year-old Japanese boy living with his nuclear researcher father, Daisuke Murakami, in British Kenya during 1941. Following Japan's attack on Pearl Harbor and the outbreak of war, they are forced to flee into the wilderness to evade British authorities. A rhino attack separates them, leaving Wataru alone. Initially timid and fearful, his character transforms over three years of survival in the wilderness. He saves Zega, chief of the Maasai tribe, by retrieving a rare healing herb, earning Zega's protection and mentorship. Under Zega's guidance, Wataru masters survival skills, spear combat, and elephant riding, evolving into a capable survivor.

During his journey, Wataru befriends Kate, a young blonde girl manipulated by an evil shaman claiming she is a goddess. Wataru and Zega rescue her, and she joins their search for Wataru's father. Their quest involves confronting hostile tribes, giant creatures like an enormous frog and massive lizard, and subterranean lizard people. The search leads them to Nazis holding Daisuke captive. A Nazi officer, Von Goering, forces Daisuke to persuade a German scientist to develop an atomic bomb. Wataru, Zega, and Kate attempt a rescue but are captured. The scientist sacrifices himself, detonating the bomb and unexpectedly opening a portal to the Mesozoic Era.

In this prehistoric environment, they face a Tyrannosaurus rex. They are saved by Dahna, a giant purple snake with implied divine connections that had aided them before. After Dahna kills the T-Rex, it transports them back to the present through a wave-like time portal. The story concludes with Wataru reunited with his father, boarding a train with Kate as the war ends.