Chapters 5 and 6 are not a letter of Rodrigues's. Rather they are the start of the second half of the book's storytelling method: third person, past tense, like the fictional researcher's voice from the prologue.
As chapter 5 begins, Rodrigues finds himself in a jail hut with several peasants. One woman, Monica, gives him a cucumber, and says that another man with them, a man with one eye, is named Juan. Soon the same old samurai who came to Tomogi appears. He gently tries to convince them to apostatize before he leaves. The old man tells Rodrigues that the lives of all the others depend on him: if he apostatizes, they will be spared.
An interpreter arrives, a Japanese man who can be the go-between for Rodrigues and the old samurai. He and Rodrigues argue with each other: the interpreter spent time in a seminary in Europe but left, and wants Rodrigues to know that Christianity is something the Japanese do not need and do not want. The interpreter confirms that Ferreira apostatized, and reveals that he now lives in Nagasaki in a mansion with a Japanese wife. Rodrigues prays, hoping he will not have to apostatize, and further despairs at the silence of God.
Rodrigues is taken as a prison on a journey of several days, by sea and by horseback, to a new prison where he is alone. In this prison he is for the first time in Japan able to be at ease and perform all his Christian duties, an irony that he is surprised by. He soon meets the other inmates of the prison, five or six of them, all Christians and being forced to do heavy labor. He asks permission to visit them. Monica and Juan are among their number. Every day he preaches to them, offers the sacraments, hears confessions, and fulfills all other duties of a priest.
One day he is told to wash and given nicer clothes. Soon the old samurai, the governor of Chikugo, arrives. They engage in a debate about Japanese being or not being able to flourish in Japan. The old man think Christianity is incompatible with Japan. It is also revealed that he is in fact Inoue.
One of the older prisoners dies of hard labor digging holes. Kichijiro arrives, begging for forgiveness and saying that if he were born in a different time he would have been a good Christian. Rodrigues feels ashamed of himself for not accepting him, as Christ would have. The four Christians left in the prison are told to trample on the fumie to apostatize. They tell them it is only a formality, and they need not do it with conviction nor have it tarnish their beliefs.
The officials do not harass the Christians, who all refuse to trample, but they call forward Juan (Chokichi is his Japanese name). They execute him and bury him in one of the holes the prisoners dug. Rodrigues is horrified to have witnessed another martyrdom and to have the world around him be so silent and unchanged by it. He feels like God is averting his eyes and being indifferent to the horrible suffering of his followers. This is too much for Rodrigues to bear. "The martyrdom of these peasants, enacted before his very eyes - how wretched it was, miserable like the huts they lived in, like the rags in which they were clothed" (196).
The idea of being born in the wrong time features prominently in this section of the book:
There had been a time when the missionaries had frequently been invited to meals at the houses of feudal lords and samurai... They had sat at clean tables, said their grace and leisurely eaten their repast. And here he was, forgetting even to pray, and pounding upon this food for dogs. His prayer was not one of thanksgiving to God; it was a prayer of petition for help; it was even an excuse for voicing his complaint and resentment. It was disgraceful for a priest to feel like this. Well he knew that his life was supposed to be devoted to the praise of God not to the expression of resentment. Yet in this day of trial, when he felt himself like Job in his leprosy, how difficult it was to raise his voice in praise of God! (154.)
This quote reveals a central conflict that Rodrigues witnesses in Christian-persecuting Japan. Weak-willed men like Kichijiro betray time and time again, but as both Kichijiro and Rodrigues say, in another time without persecution, Kichijiro might have been a good God-fearing Christian who lived a life wholly in tune with Godly principles. Similarly, in this quote, Rodrigues feels ashamed for only complaining to God, rather than praising him. Yet he is a missionary in Japan in a very different time than in the past, when the missionaries were well received, and lived in comfort. This quote shows the conflict of living in according with Christianity when everyday life is a struggle.
The theme of sin is also illuminated upon when Rodrigues is captured:
Sin, he thought, is not what it is usually thought to be; it is not to steal and tell lies. Sin is for one man to walk brutally over the life of another and to be quite oblivious of the wounds he has left behind. And then for the first time a real prayer rose up in his heart. (144.)
Rodrigues thinks this as he sits in a dark jail cell and hears the guards laughing outside, indifferent to his fate and those of other captives. For his whole life, Rodrigues has learned that sins are those that are against commandments set down by God, like stealing and lying. Rather sins are more apparent in everyday interactions that have little bearing on heavenly salvation. Rodrigues is beginning to leave the morality of religion and think about life on earth as more important than that in heaven.
The theme of West vs. East incompatibility is part of this section when Inoue and Rodrigues debate the merits of Christianity in Japan. Rodrigues says the following:
A tree which flourishes in one kind of soil may wither if the soil is changed. As for the tree of Christianity, in a foreign country its leaves may grow thick and the buds may be rich, while in Japan the leaves wither and no bud appears. Father, have you never thought of the difference in the soil, the difference in the water? (179.)
Using nature imagery, the magistrate tries to convince the priest that Christianity may be well, good and true in Europe, but its teachings have little value for Japan. It cannot flourish in a land so fundamentally inhospitable to its teachings. This is not just because of persecution: the Japanese also do not practice the same Christianity proscribed by the missionaries. Endo's use of nature imagery is an extended metaphor that points to basic incompatibilities with what Rodrigues wants for the Japanese and what might actually be best for them, according to Inoue.
More than any other theme in this chapter, however, "silence" is the most pervasive. It occurs as Rodrigues wonders why God does not speak to him as he is imprisoned, and then it occurs more forcefully when Rodrigues witnesses Juan's martyrdom and the world goes on as if nothing happened. This episode marks a deep shift in his faith:
What he could not understand was the stillness of the courtyard, the voice of the cicada, the whirling wings of the flies. A man had died. Yet the outside world went on as if nothing had happened. Could anything be more crazy? Was this martyrdom? Why are you silent? Here this one-eyed man has died - and for you. You ought to know. Why does this stillness continue? This noon-day stillness. The sound of the flies - this crazy thing, this cruel business. And you avert your face as though indifferent. This... this I cannot bear. (195.)