The officials search the village, but the Tossama have hidden everything away. Rodrigues contemplates his feeling about Kichijiro, whom he dislikes as a lowlife yet thinks might be good at heart. Rodrigues describes, for the benefits of those receiving his letter, the extreme poverty of the Japanese peasants, who are all farms that barely eke out a living and have to pay burdensomely high taxes to their local samurai.
In early July the village is searched again, and this time the guards capture the Jiisama. An informer has told them that Christians are living in this village. An old samurai man arrives in the village and asks them to turn over their Christians, and until they do, he will take hostages. Ichizo and Mokichi volunteer, which Kichijiro is forced to go. Rodrigues advises them that if they are asked to trample in the fumie, they should, to prove they are not Christians and save the rest of the village.
Mokichi and Ichizo were imprisoned, Rodrigues learns, because they would not spit on the fumie, even though they verbally apostatized. Kichijiro did, and was set free. Ichizo and Mokichi are brought back to their village and tied out at the ocean's edge on large crosses. They will die of exhaustion in a few dies from withstanding the high tide.
When they are martyred, Rodrigues has a crisis of faith. He has heard all about martyrdoms and never imagined that the world would remain so silent and God would do nothing.
Garrpe and Rodrigues part ways. Garrpe goes toward Hirado and Rodrigues boards a small boat toward a new village, but he finds that it is abandoned. He sets out on a hilly trek to find other Christians in new villages. After one day, Rodrigues sees signs on the trail of someone else (a dead fire), but does not see him or her. As he walks alone, for the first time he contemplates the fact that God may not exist, and how meaningless his life and those of the martyred Japanese would be if that is true.
Soon Kichijiro finds Rodrigues: he was the other man on the trail. Kichijiro says he will take Rodrigues to a safe place with hidden Christians. Rodrigues worries that Kichijiro may be trying to trap him and turn him in. Kichijiro offers Rodrigues salted fish, which burns his throat when there is not enough water. Rodrigues begins to feel pity of Kichijiro, whom he realizes is a weak man born into a difficult time, but who may have been fully righteous in a time when Christians could openly practice their faith in Japan.
Kichijiro confesses for his crime of Mokichi and Ichizo, and no sooner has he confessed than he begs for forgiveness again as men ride up on horseback to capture Rodrigues. They throw silver coins to Kichijiro - not nearly the 300 corns that he should have been paid - and take Rodrigues.
One quote in this chapter heralds the beginning of Rodrigues's questioning the existence of God:
I do not believe that God has given us this trial to no purpose. I know that the day will come when we will clearly understand why this persecution with all it sufferings has been bestowed upon us - for everything that Our Lord does is for our good. And yet, even as I write these words I feel the oppressive weight in my heart of those last stammering words of Kichijiro on the morning of his departure: 'Why has Deus Sama imposed this suffering upon us?' And then the resentment in those eyes that he turned upon me. 'Father', he has said, 'what even have we done?'
I supposed I should simply cast from my mind these meaningless words of the coward; yet why does his plaintive voice pierce my breast with all the pain of a sharp needle? Why has Our Lord imposed this torture and this persecution on poor Japanese peasants? No, Kichijiro was trying to express something different, something even more sickening. The silence of God. Already twenty years have passed since the persecution broke out; the black soil of Japan has been filled with the lament of so many Christians; the red blood of priests has flowed profusely; and in the face of this terrible and merciless sacrifice offered up to Him, God has remained silent. This was the problem that lay behind the plaintive question of Kichijiro. (96.)
Rodrigues has seen so much suffering and heard of even more, since the Christians in Japan began to be persecuted and forced to apostatize under pain of death. Rodrigues has not yet seen so much suffering that he is convinced of God's silence. This is revealed in the beginning of the second paragraph: he feels he should just be able to "cast from my mind" Kichijiro's sentiments. Yet his words have affected the young missionary because they speak to an issue he has been slowly coming to terms with. As the novel progresses, the theme of silence of God will become all-consuming.
As a result of this silence, Rodrigues soon begins to question God's existence, if only hypothetically. Though he still believes in God, he allows himself to consider how ridiculous all their lives and sufferings would be if there is no God. His realizations are revelatory and profound. Thousands will have suffered and died for nothing, and around the world, people are pursuing something that does not exist:
If God does not exist, how can man endure the monotony of the sea and its cruel lack of emotion? (But supposing... of course, supposing, I mean.) From the deepest core of my being yet another voice made itself heard in a whisper. Supposing God does not exist...
This was a frightening fancy. If he does not exist, how absurd the whole thing becomes. What an absurd drama become the lives of Mokichi and Ichizo, bound to the stake and washed by the waves. And the missionaries who spent three years crossing the sea to arrive at this country - what an illusion was theirs. Myself, too, wandering here over the desolate mountains - what an absurd situation! (117.)
This quote reveals, through Rodrigues's rhetoric of trying to convince himself that he still believes in God and is merely questioning for the sake of argument, that Rodrigues is seriously entertaining these notions. By emphasizing that he is just supposing these things, he actually reveals that he is truly considering them.