In the Prologue, the Jesuit missionary Christovao Ferreira, who has served 33 years in Japan, has recently apostatized. His fellow Portuguese priests are shocked and upset, since he was a pillar of Christianity in Japan and greatly revered in Rome. For much of the 1500s, missionaries enjoyed favor in Japan, but in 1587 the new regent Hideyoshi changed the policy toward Christians. By the year 1629, Christians were being persecuted in earnest and tortured to make them apostatize. Ferreira has sent back letters to Europe detailing the gruesome tortures he has witnessed.
The novel begins in 1637. Three of Ferreira's students - Francisco Garrpe, Juan de Santa Marta, and Sebastion Rodrigues - seek approval to go to Japan and investigate what happened to Ferreira and to carry on as missionaries. After a difficult months-long journey, they end up in Macao, where the priest Valigano warns them that there are to be no more missionaries going to Japan. This is because Christians have undergone terrible tortures there.
Starting after the Prologue, the first chapter onwards is told from Rodrigues's perspective, in the form of his letters now stored in a Portuguese library. When the three young missionaries reach Macao, Juan de Santa Marta is too ill to continue. Against the admonitions of Father Valignano, the Rector of the Jesuit college in Macao, they decide to continue.
Valignano has warned them about the dangers ahead: Japan is inhospitable to Christians, a new government official named Inoue has been torturing and killing Christians, and hostility from England and Dutch ships on the way to Japan will make their journey difficult. Finally Valignano relents and allows Garrpe and Rodrigues to go, especially once they reveal that they have a secret mission: to find out what happened to Ferreira.
In Macao, the two missionaries at last make the acquaintance of a Japanese man: Kichijiro, a jittery drunkard who will be their guide in Japan and help provide ties with local Christians, though he claims to not be a Christian himself. Santa Marta's heath does not improve, though they are waylaid in Macao longer than expected because their ship needs repairs from a white ant infestation.
Departure looms. Rodrigues contemplates the face of Christ and the purpose of his journey. He feels like he is at the end of the earth, but takes comfort in the face of Christ, beloved to him since childhood. Santa Marta dies of his illness, probably malaria. Garrpe and Rodrigues set sail for Japan.
The Prologue and first chapter of the novel introduce the two main narrative voices that will dominate the rest of the book. The prologue is told from an historical viewpoint, in the third person. It seems that whomever was writing would have had access to historical records and pieced together Rodrigues's unique and terrible journey to Japan. The effect of this narration style is that it lends a tale of historical fiction a realistic air.
The first chapter then takes over with Rodrigues's voice, which will continue for many more chapters. Here, the voice is epistolary: he is writing letter back home to describe his mission in Japan. This creates a sense of realism, similar to the fictionalized historian narrating the prologue. The epistolary form allows insight into Rodrigues's character.
This chapter also introduces two important themes that will recur throughout the novel: despair at God's abandonment, and the face of Christ.
"I keep turning over in my mind the thought that I am at the end of the earth, in a place which you do not know and which your whole lives through you will never visit" (46). While this quote does not explicitly reference the silence of God, it lays the framework for Rodrigues's eventual despair at God's inattention to the remote and long-suffering places he sees in Japan.
Soon after, Rodrigues comforts himself from these troubling thought by envisioning the face of Christ. This mention shows the reader the depth of his religious devotion, and especially highlights how he feels about Christ's face - which will be the reason he takes so long to accept his need to apostatize. "I feel great love for that face. I am always fascinated by the face of Christ just like a man fascinated by the face of his beloved” (47), he writes. This shows how important the face of Christ is to Rodrigues, and how closely he holds it to his heart as a comfort and a talisman. This theme will be important throughout the rest of the novel.