Shūsaku Endō’s Silence takes place in Japan during the 1600s, shortly after the Japanese government suppressed the Shimabara Rebellion, in which Christian Japanese peasants rebelled against the government’s heavy persecution. After the rebellion’s defeat, many Catholics went underground, continuing to practice their religion in secrecy. The novel begins when a young Portuguese Jesuit missionary, Sebastian Rodrigues, and his two colleagues, Father Garrpe and Father de Santa Maria, decide to set out to Japan to find out what happened to their teacher, Father Ferreira. Ferreira is rumored to have apostatized, or renounced his religious beliefs, after having gone underground in Japan and spent thirty years in Christian service there. Rodrigues finds it hard to believe that Ferreira, a highly respected member of the Jesuit community, has renounced his faith. If he has, Rodrigues wonders what this means about his faith in Christianity and the religion he has dedicated his life to.

Rodrigues, Garrpe, and de Santa Maria head to Japan by way of the Chinese port city Macao. There, they meet with Father Valignano, a rector of the Jesuit college in the city. Valignano is against sending the priests to Japan—a new magistrate, Inoue, is rumored to be especially brutal, exacting and devising some of the most brutal forms of Christian persecution ever performed. Rodrigues persists, and Valignano relents, sympathizing with Rodrigues’s desire to find out about Ferreira once and for all. The men arrange for a ship and hire a Japanese man they find wandering around town, Kichijiro, as a guide and interpreter. Kichijiro turns out to be a lazy drunk—he pretends to work when people are watching him but otherwise lies around drinking. During a violent storm, the men catch Kichijiro muttering Latin prayers and ask him if he is Catholic, but Kichijiro remains silent, though he has a pained look on his face. De Santa Maria, sick with suspected malaria, stays behind.

The men arrive at the village of Tomogi, where they find the villagers are practicing Christianity in secret. Two men in particular, Mokichi and Ichizo, are respected Christian leaders in the town. The men help situate Rodrigues and Garrpe in a charcoal hut on the hillside, away from the authorities. There, Rodrigues and Garrpe perform mass and hear confessions. Meanwhile, Kichijiro spreads the word to other towns that the priests have arrived, and villagers from other towns come to the priests’ hut. Soon, the government finds out that Christian priests have arrived, and a group of guards come to search the village. The officials demand that the town turn over the priests in three days and in the meantime select three hostages for the guards to take away. Mokichi and Ichizo volunteer, while the village selects Kichijiro as a third. Crestfallen and angry, Kichijiro joins the men in Nagasaki, where they are forced to apostatize at the magistrate’s office. Only Kichijiro apostatizes. Mokichi and Ichizo are returned to Tomogi, where they are subjected to the water torture and left to die. Rodrigues watches the whole affair from his hut, wondering why God is silent in the face of such meaningless suffering. For the first time, Rodrigues questions his faith.

Rodrigues and Garrpe decide to split up to avoid capture. Rodrigues wanders an abandoned village where he finds Kichijiro again, begging for absolution for his sin. Rodrigues is confused by Kichijiro and wonders if he’s about to trap him. His suspicions turn out to be correct—Kichijiro has led a group of soldiers to Rodrigues that entraps him and brings him to prison. At the prison, Rodrigues is surprised to find the guards allow him to practice his priestly duties. He wonders why they are treating him so kindly. Rodrigues is brought before a tribunal of samurai who cross-examine Rodrigues. Rodrigues argues his case that Christianity is a “universal truth” that deserves to be spread to Japan, but one samurai gently argues that this isn’t the case—Christianity cannot thrive in Japan, and it’s not needed there. Rodrigues is shocked to find the man arguing before him is Inoue, the man rumored for his heinous cruelty. Inoue says he doesn’t intend to kill anyone without sufficient reason, and he’s hoping that Rodrigues instead comes to reason and decides to apostatize.

Several days later, at Inoue’s request, Rodrigues is brought by the Interpreter to an overlook of the ocean. Rodrigues watches as a group of prisoners are led to the shore, where they are wrapped in straw mats and loaded onto a boat. With them is Garrpe. The guards below order Garrpe to apostatize, but he refuses. The guards then row the boat out to dump the prisoners overboard. Garrpe swims after them in a panic and drowns. As Rodrigues watches the horrible scene unfold, the Interpreter tells him that the prisoners’ blood is on the priests’ hands. To add insult to injury, he adds that Garrpe at least showed bravery, while Rodrigues sits in silence, doing nothing for the peasants. Rodrigues sits for days in prison, numb to his situation and God’s persistent silence. He is then brought to meet Ferreira, whom he learns has taken a Japanese name and is writing a book against Christianity. Rodrigues is shocked—he can’t believe his former teacher has apostatized and now works for the Japanese government. Ferreira, visibly shaken, argues that apostasy is inevitable since Christianity is incompatible with Eastern views.

Finally, Rodrigues is taken to prison in Inoue’s house. There, he struggles to decide whether to apostatize. While sitting in his cell, he hears the sounds of what he thinks is snoring, but Ferreira, who is sitting outside Rodrigues’s cell, tells him it’s not snoring but the sound of Christians being hung upside down in a pit and tortured until Rodrigues gives in. Rodrigues, overcome, decides to apostatize. He can’t bear to let any more people suffer on his behalf. Rodrigues is taken to Nagasaki, where he is given a new Japanese name and wife. He and Ferreira live out their days employed by the government helping identify smuggled Christian goods that come in via European ships. Kichijiro comes to Rodrigues’s door one last time asking for forgiveness. Rodrigues agrees, resolved that he has come to a deeper understanding of faith in his heart, and for this reason, is a true testament to the faith, even within Japan’s borders.