Father Sebastian Rodrigues is the novel’s main protagonist. He is a Catholic Jesuit missionary who travels to Japan to learn what happened with his former mentor, Father Ferreira, who is rumored to have apostatized after heavy persecution by the Japanese government. Before traveling to Japan, Rodrigues is a bold and passionate Christian, often imagining Christ’s face as a lover might imagine their beloved’s. Rodrigues is a young man and hasn’t had much experience outside Portugal or his college’s walls, so his ideas about his faith remain idealistic and romantic. Once Rodrigues gets to Japan, however, he finds his illusions shattered and his faith severely tested.

After watching several Catholic Japanese peasants die of persecution from the government, Rodrigues starts to wonder whether God exists. Rodrigues can’t understand why God remains “silent” among so many innocent deaths and is unnerved to see how the deaths of these martyrs are not glorious acts like he’s read about but rather pitiful, cruel ones. His faith is tested even more when he finally meets Ferreira and learns that Ferreira has become a true apostate and has taken on the government’s belief that Christianity can never take root in Japan. Rodrigues undergoes a complete change of identity, shedding his former beliefs about Christianity, the Japanese people, and even Christ himself. Rodrigues finds that he must surrender some parts of his ego, which is tied up in the glory of martyrdom, to truly find the meaning of Christ. Rodrigues’s character demonstrates the issues of faith and doubts that plague humans when their ideals are confronted by experience.