Two months later, Rodrigues writes another letter (Chapter 2) that details his life since arriving in Japan. They set sail at the end of April, and at first have good weather, but eight days into their journey a strong storm begins. It lasts through the night, and in his terror, Kichijiro mutters some unmistakably Latin prayer words. He still denies being a Christian when Garrpe questions him.
They sight land soon after and get off the ship under cover of darkness. Kichijiro runs off to find Christian villages, who great them with torches and lead them to a safe house. The next day they climb up a mountain where they will be living in a charcoal hut. They learn that they are in Tomogi, a town near Nagasaki.
They also find out about the way that the Japanese Christians nearby have been practicing their religion for the past 6 years since any priests have lived among them. They have devised their own religious order, led by the Jiisama, who baptizes children; below him are the Tosama group, who teach and lead prayers; and below them are the Mideshi, or ‘helpers’.
Chapter 3 is a letter that Rodrigues wrote in June of the same year. Rodrigues feels like he is making a big difference in Japan for the Christians, who have been for so long lost without a priest. He details the hard lives of the peasants, who must pay harsh taxes and live difficult day-to-day lives. More than that, officials, who inspect villages and offer payment for informers, also heavily persecute them.
The rain pours for days in the rainy month of June, and Garrpe tries to keep their spirits up. They live in a tiny hut full of insects and get small amounts of food from their Christian flock. When the rains end, the two step outside and believe two men at the top of a neighboring hill are watching them. One of the peasants, Ichizo, is very concerned and along with one of the Tossama digs a hiding place in their hut for the missionaries.
Five days later, after performing a baptism, two peasants from Fukazawa arrive, wanting to confess their sins. They admit that they were the two men watching them. They say that Kichijiro, a Christian from their village, told them the missionaries were there. They say that their village along with neighboring ones have kept to Christian beliefs as they have not been routed out by the authorities. Rodrigues agrees to go with them to their village, Goto, and b a priest there. Garrpe will stay behind.
There Rodrigues is kept busy with a constant stream of baptisms, confessions, and Sunday Mass. Upon his return journey to Tomogo, a frantic Mokichi and Kichijiro greet him; he says that there are guards in the village.
The image of planting a seed of Christianity appears for the first time in this chapter. "Yes, the seed had been sown; it sprouted forth with vigor; and now it was the great mission of Garrpe and myself to tend it lest it wither and die” (55), Rodrigues writes. This likening of Christianity to a seed creates figurative language that will later be used in Rodrigues and Inoue's verbal spars. Here, it makes Christianity seem fragile yet pure in its new home of Japan.
This language further appears in the chapter when Rodrigues thinks about how Christianity has managed to stick in Japan despite persecution. "I recalled the words of the Gospel that some seed fell upon good ground and springing up it brought forth fruit, some tenfold, some thirtyfold...” (56). Rodrigues is reminded of this Gospel by the way that the Japanese kept alive their faith by making their own religious organization of Christianity. This language enhances the nature imagery used to describe Christianity. It reveals how Rodrigues views his purpose: one of nurturing something that is good for all.
Water imagery, a theme in the novel that is linked to the ocean, occurs in chapter 3. Rodrigues describes Christianity "penetrat[ing] this territory like water flowing into dry earth" (61). This links the water imagery of the novel, which usual is in reference to the ocean and by extension God's silence, with the nature imagery, which positions Christianity as something to be nurtured and grown.
The beginning of Rodrigues questioning the will of God also occurs in these pages. This will become the crux of the novel: Rodrigues's inability to reconcile the harsh lives of Japanese Christians with the God who is supposed to watch over them all. "Why has God given our Christians such a burden? This is something I fail to understand” (65). This is foreshadowing of an important theme in the novel: Rodrigues grappling with his faith and the potential non-existence of God.
Rodrigues further illuminates his questions of faith with a commentary on the lives of the peasants he interacts with. At a baptism: "This child also would grow up like its parents and grandparents to eke out a miserable existence face to face with the black sea in this cramped and desolate land; it, too, would live like a beast, and like a beast it would die. But Christ did not die for the good and beautiful. It is easy enough to die for the good and beautiful; the hard thing is to die for the miserable and corrupt - this is the realization that came home to me acutely at that time” (71).
This quote reveals the two sides of Rodrigues's battle with his life as a missionary amidst great suffering. If God exists, then the missionaries are doing the most important work in the world. They are saving the very souls that Christ died for. But if God remains silent - if God does not care, or does not exist - then these peasants are living a hard life that will lead to nothing but the void of death. In this quote, Rodrigues has not yet lost hope in God's existence, so he sees his baptism of a small Japanese peasant baby as the kind of difficult work that Christ would have wanted his followers to pursue.