Father Rodrigues and Father Garrpe have just received bad news: their former teacher, Father Ferreira, has renounced his faith after being captured by the Japanese government. Upset and confused, the two priests decide to defy the country's ban on Christianity to learn the truth themselves.
The fearless fathers manage to get into Japan with the help of Kichijiro, a Japanese expatriate they meet in Macau. Kichijiro introduces them to a host of devout Japanese Christians who are beyond psyched to have some real live priests around. Unfortunately, the government catches wind of this and decides to execute several villagers as punishment. Kichijiro is only able to escape by renouncing his faith.
Garrpe and Rodrigues split up to evade the authorities. While wandering, Rodrigues finds Kichijiro once again, who tells the priest that he'll lead him to more Christians. Unfortunately, all he actually does is sell Rodrigues out and turn him over to the authorities.
Rodrigues spends the next several months in a cell. He eventually discovers that Garrpe had been captured as well. Garrpe refuses to renounce his beliefs and ends up dying for them, more or less. Rodrigues also learns that Ferreira is alive, having been integrated into Japanese society after his fall from grace.
Our boy Rowdy Rodrigues (okay, he's not so rowdy) is understandably bummed about this. Finally, after much internal debate, he decides to renounce his faith, too—after all, it's the only way he can prevent more Japanese Christians from being brutally executed. Like his former teacher, Rodrigues lives out the rest of his days with a Japanese name—Okada San'emon—and as a Japanese citizen.