Inoue and Rodrigues meet again and once more debate the merits of Christianity in Japan. Inoue does not think Christianity is evil, but rather that it is unsuited to Japan and also has been used by European powers in their perpetual rivalries.
After Inoue leaves, Rodrigues goes back to his cell-hut and thinks about his plight. He even compares some of it to the trials of Jesus, whom he loves so much, but grows uneasy when he reflects that he has not suffered a lot in his captivity. He worries that Inoue’s plan is to make him comfortable and complacent and thus more likely to apostatize. He is treated well, able to perform his priestly duties, and gets three meals a day.
Ten days after Inoue’s visit, he sees the three remaining Christians, including Monica, being taken away for forced labor. The next day he is taken to Nagasaki. He sees the interpreter again, and soon thereafter, Garrpe is brought in along with the three Christians.
The three Christians are rolled out to sea covered in straw wrappings, where they will sink and die – even though they apostatized. The only way for them to be saved would be for Garrpe to apostatize. Rodrigues has an inner morality debate about whether or not Garrpe should apostatize. In his mind he wants Garrpe to apostatize, but he cannot find the mental strength to shout it out loud.
The three Christians, including Monica, are pushed out to sea and drown. Garrpe tries to swim out to their boat and save them, but he is too late and also drowns among the waves. The interpreter expresses shame toward Rodrigues, saying he is weak-willed and does not deserve to be called 'father', for imposing a religion upon the Japanese that is causing them nothing but suffering.
Rodrigues spends days in silent depression. He is eventually taken to meet Ferreira, now called Sawano Chuan. Ferreira tells Rodrigues that he spends his days writing on useful subjects to the Japanese, like astronomy and Western medicine. The interpreter, who has accompanied Rodrigues, reveals that Ferreira is also writing book that deny Christianity.
Ferreira tells Rodrigues to apostatize, and warns him about 'the pit' – a torture method Inoue invented, where one is suspended upside down in a pit full of waste, with cuts behind the ears so that blood drains out of the body slowly. Ferreira also tells Rodrigues that the Christianity practiced by the Japanese was never truly the Christianity of the Church: it was a corrupted form, since the Japanese, according to Ferreira, never had and never will have a concept of God.
In this chapter Rodrigues has to contend with whether to sin against God or against human morality, in the scene where the three Christians are going to be drowned:
“If Garrpe shook his head in refusal, these three Christians would sink like stones in the bay. If he gave into the solicitations of the officials, this would mean the betrayal of his whole life. What was he to do? (215.)
This is an example of the theme of sin: what constitutes a sin, one against God, or one against human morals? Rodrigues shows clear conflict in this encounter. In his head, he screams for Garrpe to apostatize; yet he cannot find it in himself to say these words aloud, and Garrpe dies for his faith, as do the peasants. This plunges Rodrigues into a deep depression where he ultimately questions his faith even more.
This depression and doubt in God leads to a furthering of the theme of silence. ”The sea stretched out endlessly, sadly; and all this time, over the sea, God simply maintained his unrelenting silence,” Rodrigues thinks (222). “Did God really exist? If not, how ludicrous was half of his life spent traversing the limitless seas to come and plant the tiny seed in this barren island!” (223.) Although Rodrigues regains his spirit after the night ends, he now looks at God as “an object of fear and perplexity,” rather than the God of his youth who gave “harmony and living joy” (ibid.).
Silence also appears not just as God being silent in the face of suffering, but also in the face of apostasy. Ferreira has become Sawano Chuan, a refuter of Christianity, yet “Lord, you are still silent. You still maintain your deep silence in a life like this!” (Ibid.). Rodrigues appears just as shocked at this silence as he is at the silence for the martyrs. There are many ways God could have made his wishes known, Rodrigues realizes – and so many opportunities.