The novel Silence opens with a prologue that describes the historical, religious, and social background of the novel. The setting is Japan in the 1600s, shortly after the Shimabara Rebellion, in which Christian peasants revolted against the government for heavy persecution. European Christian missionaries had enjoyed an influence in Japan, spreading their religion for several decades, but after a regime change, Christians are no longer welcome. Three Portuguese Jesuit priests, including Father Rodrigues and Father Garrpe, decide they want to head to Japan anyway to learn about the fate of their former teacher and mentor, Father Ferreira, who is rumored to have apostatized. If he has, the men will face a crisis in their faith. They also want to head to Japan to restore the Church’s name. With this, the novel’s exposition is laid out.

The next several chapters are made up of letters written by one of the priests who are venturing to Japan, Sebastian Rodrigues. The narration shifts from third person to first person through Rodrigues’s accounts. Rodrigues is the protagonist of the novel. Out of the three priests who set off toward Japan, he is the most bothered by Ferreira’s apostasy and is the most motivated by the lost glory of the Church. As revealed in his letters, he has a bold and passionate belief in Christ and is willing to risk his life to save Christ’s name. It is clear that Rodrigues fashions himself as a heroic figure and also harbors a fair degree of arrogance and prejudice. When he first meets a group of Christian Japanese peasants, he struggles to distinguish between their faces and finds it unseemly that the words of his faith are uttered by crude people. As Rodrigues will find, not only his preconceived notions about Japan but his faith itself will be challenged by these interactions.

Over the next few chapters, the rising action occurs, and the narration shifts from the first person through Rodrigues’s letters back to the third person. Throughout these chapters, the priests find themselves witness to more and more senseless torture of the Christian peasants and struggle with whether to apostatize. It’s not long before the government discovers the priests’ presence and comes searching for them. But instead of punishing the priests directly, the country’s magistrate, Inoue, who is also the novel’s antagonist, has devised a more effective form of punishment—torturing the peasants on the priests’ behalf. Kichijiro, a Japanese fisherman whom Rodrigues hires to take them to Japan, proves to be a thorn in Rodrigues’s side, the foil to Rodrigues’s character, betraying Rodrigues’s presence to the officials and then asking Rodrigues for forgiveness over and over again. Rodrigues considers Kichijiro to be his Judas, a person who is sent to test his faith and ability to forgive. Rodrigues is finally imprisoned and is surprised to find that the guards have no problem with him continuing to practice his faith with his fellow inmates. He learns that Japan doesn’t have a problem with Christianity itself, but rather with the problems it causes for the country’s government. The issue is a pragmatic one, not an ideological one. This raises even more questions for Rodrigues and his struggle, for he might be fighting for a lost cause.

The priests continue to have their faith tested. Garrpe, who is forced to witness a group of peasants tortured on his behalf, doesn’t apostatize but drowns trying to save them. Looking on is Rodrigues, horrified and wondering if this was the right decision. Rodrigues, who has struggled throughout the novel with God’s “silence” in the face of senseless torture, wonders if he should abandon his faith altogether and whether God really exists. His faith is starting to be severely tested. Finally, Rodrigues meets with Ferreira and learns the bitter truth. Ferreira has indeed apostatized, and he has taken on a new Japanese identity. Ferreira tells Rodrigues that his fight with his faith is not over Christ but his perceptions of Christ’s work. Still resistant to renouncing his faith, Rodrigues is imprisoned. When he learns that the sounds he hears through the prison walls are the sounds of Christians being tortured on his behalf, he finally gives in. The climax of the novel occurs, and Rodrigues apostatizes. He can no longer endure others suffering because of him. He can no longer endure God’s silence.

The falling action is told mostly through a series of diaries and accounts from men within Rodrigues’s sphere. A Dutch clerk notes that Rodrigues and Ferreira have been hired to identify Christian objects smuggled on his country’s ships coming into Japan and that they do their jobs well. Rodrigues is given a new Japanese name and wife and is put under house arrest for the remainder of his life, only being allowed out with the magistrate’s permission. The men conclude their lives as Japanese men, assimilated into their new culture. The conclusion of the novel suggests, however, that Ferreira and Rodrigues still hold their faith in their heart, but a newer, deeper version of it through their experiences.