Chapter 10 is written not from the perspective of Rodrigues or an omniscient narrator in the future, but rather from the perspective of the diary of Jonassen, a clerk at the Dutch firm in Dejima, Nagasaki. The year is 1644 and he relates small tidbits about each day - ships comings in and out of the port, and the goods they carry.
One report on June 9th talks of a family where a coin with a saint on it was found in their house. The parents were executed and the children put into jail and eventually executed, and the apostatized Padre Rodrigues tried to get for mercy for them without success.
Soon after Jonassen is questions again, because Sawano Chuan/Ferreira and Rodrigues told government officials that Dutch vessels from India would carry priests from Macao to Japan. Jonassen is warned that his Firm will be in great trouble if a priest comes to Japan on any of the Dutch ships. Jonassen has to tell the crew on Dutch vessels that if they have anything Catholic on the, they must throw it away or be punished.
In November 1945 Jonassen's diaries continues as usual, with typical reports about "Chinese junks clearly the port," and so on (287). Jonassen continues to have to deal with bouts of anti-Catholicism, like assuring the government that the Dutch are not Catholic, and having to confirm that certain items found in homes are of Catholic origin and that the inhabitants can be justly punished. In January he observes a fumie apostasy display of a small family.
The chapter now switches to third person, focusing on Rodrigues. Rodrigues is summoned to see Inoue, Lord of Chikugo. Inoue tells him he has a house and wife of a recently deceased man for Rodrigues to take over, in Kobinatacho, Edo. He will take over the dead man's name: Okada San'emon. Inoue once more tells Rodrigues that the Christianity of Japan and the God that they pray to is not the Christian God that the missionaries brought over; the "swamp" of Japan has changed the religion.
That night Kichijiro comes to him asking to have confession. As Kichijiro asks forgiveness for trampling on the fumie, and acknowledges that he is a weak man, Rodrigues's thoughts turn to his own apostasy. He tells God that he "resented your silence," and hears God telling him that he was not silent, but rather suffered alongside him (297). Rodrigues asks God a question that has always bothered him: why did he tell Judas to go away? God replied that he told Judas what to do (betray him). Renewed, Rodrigues releases his judgment of weak and strong people, and hears Kichijiro's confession. He knows he is cut off from the church but feels in his heart as strong a love for God as ever. "He loved him now in a different way from before" (298).
The Appendix is the diary of an officer at the Christian Residence, or Rodrigues/Okada San'emon's house. The diary lists the members of the household, Rodrigues's activities writing a disavowal of Christianity, a drama involving Kichijiro and Christian items found in his possession. Christians continue to be persecuted, and the appendix contains records of jailings. Finally San'emon's death is recorded. He died of illness on July 25th in the 9th year of Enpo, at the age of 64. He had lived in his Christian Residence for 30 years. His body is cremated and he received a posthumous Buddhist name.
The last chapter and appendix combine many viewpoints to show the end of Rodrigues's story. There is the diary of Jonassen, the historian's approach to the second half Chapter 10, and then the family records in the appendix. The effect of all these perspective, combined so closely together at the end of the novel, is once more to give the historical fiction book a sense of realism, as though its contents were truly compiled from historical sources.
The theme of Japan being a swamp that is inhospitable to Christianity occurs again in Chapter 10. Inoue tries to make Rodrigues see his point of view, long after his apostasy: "Christianity simply cannot put down roots here," Inoue says, again using the same nature imagery he has used before to draw a metaphor about how the soil of Japan will never let the sapling of Christianity grow. "Father, you were not defeated by me," Inoue says, "You were defeated by this swamp of Japan" (292).
This language extends into the rest of Inoue and Rodrigues's conversation. Inoue tells Rodrigues that there are still Christians in Japan, but without any priests left, he is comfortable with not prosecuting them - especially because their version of Christianity has been warped from its original message: "If the root is cut, the sapling withers and the leaves die... The Christianity you brought to Japan has changed its form and has become a strange thing" (294). This nature imagery reinforces the extended metaphor, developed throughout the novel, that shows how it is natural for Christianity to be unable to find purchase in Japan.