The adventure unfolds as John, the two young boys George and Harry, and their native companions Uraso and Muro navigate unknown territories on a remote South Sea island. Faced with hostile tribes, cannibalistic customs, and elaborate sacrificial rites, the group relies on clever strategy, psychological influence, and modern inventions rather than brute force to subdue conflicts and win the trust of native chiefs. Their explorations lead them through dense forests, across treacherous mountain ridges, and eventually into dark, forbidding caverns that hold ancient archeological secrets. Inside these mysterious caves, they discover a copper box containing a skull with cryptic inscriptions, shedding light on old buccaneer legends and long-lost expeditions.
Along the way, they rescue long-suffering captives, including a white man named Ephraim Wilmar who has lived among a northern tribe for decades, eventually becoming their respected leader. As the various island tribes are united through peaceful diplomacy, agriculture, and education, the characters establish regular communication with the outside world via their vessel, the Pioneer. The overarching mystery of the lettered skulls and hidden treasure charts slowly unravels as former adversaries reappear and long-buried secrets come to light. Ultimately, the narrative celebrates the triumph of reason, mutual aid, and self-reliance over superstition, leaving the island inhabitants on a path toward lasting peace and community development.