Young Portuguese Jesuit, Sebastião Rodrigues (based on the historical figure Giuseppe Chiara) is sent to Japan to succor the local Church and investigate reports that his mentor, a Jesuit priest in Japan named Ferreira, based on Cristóvão Ferreira, has committed apostasy. Half of the book is the written journal of Rodrigues, while the other half of the book is written either in the third person, or in the letters of others associated with the narrative. The novel relates the trials of Christians and the increasing hardship suffered by Rodrigues.
Fr. Rodrigues and his companion Fr. Francisco Garrpe arrive in Japan in 1639. There they find the local Christian population driven underground. To ferret out hidden Christians, Security officials force suspected Christians to trample on a fumie, a crudely carved image of Christ. Those who refuse are imprisoned and killed by anazuri (穴吊り), which is by being hung upside down over a pit and slowly bled.
Rodrigues and Garrpe are eventually captured and forced to watch as Japanese Christians lay down their lives for the faith. There is no glory in these martyrdoms, as Rodrigues had always imagined - only brutality and cruelty. Prior to the arrival of Rodrigues, the authorities had been attempting to force priests to renounce their faith by torturing them. Beginning with Fr. Ferreira, they torture other Christians as the priests look on, telling the priests that all they must do is renounce their faith in order to end the suffering of their flock.
Rodrigues' journal depicts his struggles: he understands suffering for the sake of one's own faith; but he struggles over whether it is self-centered and unmerciful to refuse to recant when doing so will end another’s suffering. At the climactic moment, Rodrigues hears the moans of those who have recanted but are to remain in the pit until he tramples the image of Christ. As Rodrigues looks upon a fumie, Christ breaks his silence:
“Trample! Trample! I more than anyone know of the pain in your foot. Trample! It was to be trampled on by men that I was born into this world. It was to share men’s pain that I carried my cross.”
Rodrigues obeys, and the Christians are released.