In 17th-century Portugal, the Roman Catholic Church learns that Father Ferreira, a highly-respected missionary who has worked in Japan for over 20 years, has somehow been made to commit apostasy, renouncing Christianity by stamping his foot on a picture of Jesus Christ. The Church is both confused and disturbed by this news, and several of Ferreira’s former students (he was a seminary professor before going to Japan) launch an expedition into Japan to continue Ferreira’s former evangelistic work and discover the truth about his apostasy, even though the Japanese government brutally oppresses Christianity.
Fathers Rodrigues and Garrpe, former students of Ferreira, are Portuguese priests in their late 20s. The pair travel from Portugal to China, hoping to find a covert way to reach Japan. While there they are joined by Kichijiro, a pitiful and drunken man about their age whom they suspect is a Christian, though he adamantly denies it. A Portuguese superior of the Church warns them of a magistrate named Inoue, a particularly cruel and devilish persecutor, but nevertheless helps Rodrigues and Garrpe commission a Chinese ship and crew. They smuggle themselves and Kichijiro onto the shores of Japan, landing in the mountains near Nagasaki.
Kichijiro helps the priests find an isolated Christian village called Tomogi, though the Japanese peasants have not had a priest for six years. The villagers shelter the priests, hiding them in a charcoal hut atop a nearby mountain, where the priests wait silently during the day and then minister to the villagers at night, only one or two at a time. Despite their attempts to remain hidden, Kichijiro—whom the priests discover is a Christian who apostatized years before—spreads word to other villages that there are foreign priests in Japan once again. Villagers from a neighboring island beg the priests to visit, so Rodrigues travels there alone. When he returns, officials of the Japanese government are in Tomogi, having been informed that there are practicing Christians present, though they don’t yet know of the priests. Three men—including Kichijiro—are chosen to travel to Nagasaki with the officials, and apostatize before the magistrate’s office to prove that their village is not Christian. Although Rodrigues advises them to apostatize, only Kichijiro does so, and the other two men are returned to the village where they are tortured for several days until they die of exhaustion in front of the villagers. The priests are disturbed, feeling as if they have brought suffering upon the villagers, and when news arrives that the officials are preparing to search the mountains as well, Rodrigues and Garrpe decide they must flee. They split up, hoping that at least one priest may survive and minister to Japan. As Rodrigues flees, he wonders why God does not speak or intervene when his followers suffer.
Rodrigues wanders into the hill country, believing that he will be safer there, and soon runs into Kichijiro, who fled Tomogi after he apostatized. Kichijiro asks the priest for absolution for his sin, but even as he does so sells Rodrigues out to Japanese officials, who capture the priest and take him to a newly-built prison. Other Christians are imprisoned there as well, and the guards surprisingly allow the priest to visit them twice a day to pray, hear confession, and perform his priestly duties. Thus, prison feels both restful and productive to the priest; he no longer has to hide and is allowed to fulfill his function. After Rodrigues has been imprisoned for some time, the magistrate Inoue and several of his samurai arrive to cross-examine him. Rodrigues is surprised to learn that Inoue, whom he had pictured as devilish and conniving, is in fact a kind-faced, gentle old man who is not intimidating or cruel-looking in the slightest. Inoue and the samurai converse amiably with the priest, expressing their opinion that Japan has no use for Christianity, and Christianity in turn is not well-suited to Japan. When the cross-examination is over, Inoue asks the priest to simply think over what he has said and takes his leave. Kichijiro arrives at the prison and volunteers himself for arrest, but when threatened with death, apostatizes again and is released.
Several days later, the guards—at Inoue’s request—bring the priest to an overlook from which he can see the seaside. As the Rodrigues watches, he sees the Christians from the prison gathered along with Garrpe, who he has not seen since they both fled Tomogi. Rodrigues is too far away for Garrpe to see or hear him, but Rodrigues watches as the prisoners are wrapped with straw mats that confine their arms and legs and loaded into a boat that takes them off-shore over the deep water. As an official explains to Rodrigues, Garrpe is being asked to apostatize, and if he does not, the Japanese Christians—though they themselves have apostatized—will be pushed into the sea and drowned. Rodrigues begs Garrpe in his heart to apostatize, but Garrpe does not. As the Christians are pushed into the ocean, Garrpe tries to swim out to meet them and willingly drowns himself. Rodrigues is horrified, and the official that is with him tells him that their blood is on his hands, since he is a priest. Rodrigues is again haunted by God’s silence.
Rodrigues becomes numb and ceases eating or speaking, staring only at the wall as he thinks about God’s refusal to intervene and the futility of all the deaths he has seen. While he is in this state, he is brought into Nagasaki to meet Ferreira, whom he learns has been living there with a Japanese wife and children for the past year. Ferreira seems defeated, but explains to Rodrigues why he came to believe, after 20 years of missionary work, that Christianity can never truly exist in Japan. Japan’s Eastern culture is simply too incompatible with Western Christianity, and the religion either withers away or becomes something else entirely. Ferreira is visibly pained, even broken. Still, his arguments are confusing and overwhelming for Rodrigues. But when he still will not apostatize, the priest is taken to the magistrate’s house where he is locked in a small, dark cell, and forced to listen to the sound of Christians being tortured in the courtyard.
After being left alone there for several hours, listening to the sounds of suffering, Ferreira again visits Rodrigues and explains that the only way to end the suffering of the Japanese Christians is for Rodrigues to humiliate himself, destroy his pride, and apostatize, exclaiming that Christ himself would apostatize out of love for the suffering. Rodrigues, broken, finally agrees. As he holds his foot above the image of Christ, preparing himself to betray his faith, he hears Christ speak to him, telling him that it is okay to trample on him, since Christ came to earth to be trampled on by men and will be present with the priest in his suffering. Still pained but emboldened by Christ’s words, Rodrigues apostatizes.
Rodrigues is given a home and a wife in Nagasaki, as Ferreira was. He is employed by the Japanese government to help block Christians from smuggling religious items into the country. The Catholic Church in Portugal has learned of his betrayal and expelled him, taking away his right to minister as a priest. Although he is treated well by Inoue and the Japanese officials, his spirit is crushed. However, when Kichijiro arrives on his doorstep once more asking to confess and receive the priest’s absolution, Rodrigues agrees, deciding that although he is rejected by his former brethren, he is not rejected by God, who was not silent but suffered alongside him, and to whose presence the priest’s entire life gives testimony.
