In the 17th century, two Portuguese Jesuit priests, Sebastião Rodrigues and Francisco Garupe, travel to Japan to find their mentor, Father Ferreira, who is rumored to have renounced his faith under torture. Upon arrival, they witness the brutal persecution faced by local Christians under the Tokugawa shogunate, which has banned Christianity. The priests navigate a perilous landscape, ministering to covert Christians in isolated villages while evading capture. They are guided by Kichijiro, a conflicted and unreliable ex-Christian who perpetually seeks forgiveness for his transgressions.

As they move deeper into Japan, Rodrigues and Garupe face increasing danger, grappling with their faith amid unspeakable suffering. They become separated, each enduring unique trials that challenge their mission and resolve. Rodrigues is eventually captured and forced to confront the harsh reality of his purpose and the lasting impact of his presence on the Japanese Christians. The intense struggle between faith and silence, hope and despair, permeates their journey as they seek answers in a land hostile to their beliefs. The narrative deeply examines the themes of faith, apostasy, and the clash of cultures.