Act I: In a church in Macau. A young Portuguese missionary, Rodrigo, wants to go to Japan, but Father Valignano tries to persuade him to give up since there is strong oppression of Christians in Japan. However, Rodrigo manages to leave for Japan with a Japanese guide, Kichijiro. His goal is to find his fellow missionary, Ferreira, who seems to have disappeared in Japan, and to help the Japanese Christians.
Successfully entering Japan by stealth, Rodrigo starts his missionary work at Tomogi village in Nagasaki and prays with the villagers. However, the happy days devoted to piety do not last long. Officials come to apprehend the villagers and force them to take a test to prove there are not Christians. Mokichi and other villagers who refused to tread on a picture of Christ are crucified in the sea. Mokichi's lover, Oharu, grieves and loses her mind. The crucified villagers pray as they drown in the waves. Presented with the hard reality the Christians have to face, Rodrigo is devastated and his own powerlessness tortures him. Just then, officials appear. Kichijiro has traded his own safety for Rodrigo's whereabouts. Rodrigo is taken captive.
Act II: In prison, Rodrigo hears news about Ferreira. He has abandoned Christianity, taken a wife and lives under a Japanese name. Inoue, Lord of Chikugo, and in charge of Nagasaki, declares that Rodrigo's Christian followers will be cast into the sea if he does not give up Christianity like Ferreira did. Rodrigo has to watch the Christians being thrown into sea. Ferreira arrives in prison to persuade Rodrigo to abandon Christianity. Rodrigo is disgusted at the change Ferreira has undergone and drives him out. On the evening before his execution, Rodrigo compares his feelings with Christ's on the cross. He is irritated by the snores of the drunken gaolers, but is aghast when he learns that the noise was the groans of the hanged Christians. So many Christians have had to suffer because of him. He prays to God, but instead of an answer, all he gets is silence. With his heart tearing, he takes a step to tread on the image of Christ.