Plot

In the 17th century, two Portuguese Jesuit priests travel to Japan in an attempt to locate their mentor, who is rumored to have committed apostasy, and to propagate Catholicism.

Intent on investigating the truth behind Father Cristovão Ferreira's abrupt end of correspondence, the devout Portuguese Catholic priests, Sebastião Rodrigues and Francisco Garupe, set off to Japan, in 1633. In great disbelief, as the rumours of Ferreira's apostasy still echo in their minds, the zealous Jesuit missionaries try to locate their mentor, amid the bloodshed of the violent anti-Christian purges. Under those circumstances, the two men and the Japanese guide, Kichijiro, arrive in Japan, only to witness firsthand the unbearable burden of those who have a different belief in a land founded on tradition. Now--as the powerful Grand Inquisitor, Inoue, performs hideous tortures on the brave Japanese Christians--Father Rodrigues will soon have to put his faith to the ultimate test: renounce it in exchange for the prisoners' lives. There, in the ends of the world, a subtle change has begun; however, why is God's silence so deafening?—Nick Riganas

In the seventeenth century, in Portugal, the Portuguese Jesuit priests Sebastião Rodrigues and Francisco Garupe ask permission to Father Alessandro Valignano to travel to Japan to investigate the rumors that their mentor Father Cristóvão Ferreira had committed apostasy abandoning his Catholic faith after being tortured by the shogunate. They meet the alcoholic fisherman Kichijiro that agrees to guide them to Japan. When they arrive at a small village, they learn that the Christians residents live hidden in caves since the Inquisitor kills any villager suspect to be Christian. Along the days, Rodrigues and Garupel propagate Catholicism among the villagers and try to find a lead to Ferreira. But when the Inquisitor arrives in the village with his men, the lives of the residents and the priests will change.—Claudio Carvalho, Rio de Janeiro, Brazil

The young Portuguese Jesuit priest Cristóvão Ferreira witnesses the mortal torture of five missionaries. The priest is helpless in the presence of Japanese authorities conducting the torture to try to assist his colleagues in any way. A few years later, at St. Paul's College, Macau, an Italian Jesuit priest, Alessandro Valignano, receives news that Ferreira renounced his faith in Japan after being tortured. In disbelief, Ferreira's Portuguese pupils, Jesuit priests Sebastião Rodrigues and Francisco Garupe, set off to find him. Kichijiro, an alcoholic fisherman who fled Japan to save himself, agrees to guide them.

In 1633 the young Portuguese Jesuit priest Cristóvão Ferreira (Liam Neeson) witnesses the mortal torture of Japanese converts he has been trying to bring to the Christian faith. The priest appears to be helpless in the presence of Japanese authorities conducting the torture to try to assist his converts in any way. The authorities pour boiling water on the faces and bodies of the converts, but do not harm Ferreira. The converts were crucified, and water was dropped from ladles which had tiny holes in them, so the water would come out slowly and the pain would be prolonged. The converts refused to give up their faith and some of them endured torture for 33 days.

A few years later, at St. Paul's College, Macau, an Italian Jesuit priest, Alessandro Valignano (Ciarán Hinds), receives news that Ferreira renounced his faith (apostasy) in Japan after being tortured. Ferreira's last letter (in which he describes the growing torture on the converts, but nothing about himself) reached Alessandro several years after being dispatched and was smuggled out and handed over by a Dutch trader. The trader told Alessandro that Ferreira gave up his faith and now lives as a Japanese.

In disbelief, Ferreira's Portuguese pupils, Jesuit priests Sebastiao Rodrigues (Andrew Garfield) and Francisco Garupe (Adam Driver), set off to find him. Rodrigues says that the news of Ferreira giving up his faith has not been validated and refuses to believe it. He and Garupe argue that if the news is true, it is even more urgent as the Jesuits need to continue their mission. And they need to rescue the soul of Father Ferreira as it is damned if he has renounced his faith.

Kichijiro (Yosuke Kubozuka), an alcoholic fisherman who fled Japan to save himself, agrees to guide them. Kichijiro is seeking redemption, as he renounced his faith to save himself while the rest of his family was put to death.

Arriving in the 1639 Japanese village of Tomogi, the priests are dismayed to find local Christian populations driven underground. The priests stay hidden inside their hut for several months, even though the village converts come to them for confessions and to baptize their newborn. One day, they step out to soak some sun, but are spotted by 2 villagers.

Both priests are then shocked when a samurai searching for suspected Christians, whom the villagers refer to as the "Inquisitor". The villagers hide the two priests, but they are horrified when officials of the shogunate arrive to ferret out hidden Christians and force them to step on a Fumi-e, a carved image of Christ. The Inquisitor straps some of the villagers (who refuses to step on the Fumi-e) to wooden crosses by the ocean shore, where the tide eventually drowns them. The bodies are then cremated on a funeral pyre which the priests understand is done to prevent a Christian burial.

Garupe leaves for Hirado Island, believing that their presence forces the shogunate to terrorize the village. Rodrigues goes to Goto Island, the last place Ferreira lived, and finds it destroyed. Wandering around Goto, he struggles over whether it is self-centered to refuse to recant when doing so will end others' suffering. He eventually reunites with Kichijiro in 1643, who betrays him into the hands of the samurai. An old samurai, who had earlier accompanied the "Inquisitor" to Tomogi, tells Rodrigues that other captured Christians will suffer unless he renounces his faith. Rodrigues is forced by the Inquisitor, the Daimyo Inoue Masashige (Issey Ogata), to watch as converts are tortured.

Rodrigues is taken to Nagasaki, where he is imprisoned with many Japanese converts. At a tribunal, he is told Catholic doctrine is anathema to Japan. Rodrigues demands to see Governor Inoue Masashige (Issey Ogata), who he learns, to his dismay, is the old man seated before him in charge of the proceedings. Rodrigues is returned to prison, and Kichijiro soon arrives to be imprisoned as well. He explains to Rodrigues that court officials threatened him in order that he betray Rodrigues. Kichijiro then says he is a Christian and asks to be absolved of his betrayal through a confession, which Rodrigues reluctantly grants him. He later is released after being told to step on a Fumi-e (a crudely carved crucifix), an act symbolizing rejection of the faith.

Later, Rodrigues is brought under guard to the shoreline to await someone. In the far distance, he witnesses an emaciated Garupe and three other prisoners approaching on the shoreline under separate guard. Still in the distance, the three other prisoners are taken offshore on a small boat and are about to be drowned from the boat one-by-one as an inducement to get Garupe to renounce his faith. Rodrigues is restrained by guards on shore as he watches Garupe refuse to apostatize. He then sees the desperate Garupe drowned next to the other three prisoners when he attempts to swim offshore trying to rescue the last prisoner from being drowned. Rodrigues' faith in God is shaken.

Rodrigues is taken to meet Ferreira, who has assimilated into Japanese society. Ferreira apostatized while being tortured to save his fellow Christians, and now believes that Christianity has no place in Japan. That night, Rodrigues is brought to watch five Christians being tortured. He learns that they have already apostatized but will continue to suffer until he also abandons his faith. Rodrigues struggles over whether it is self-centered to refuse to recant when doing so will end others' suffering. He hears what he thinks is the voice of Jesus, giving him permission to step on the Fumi-e, and he does.

Rodrigues takes a Japanese name and wife and is tasked by the Inquisitor to assist Ferreira in his efforts to prevent Dutch traders from smuggling Christian paraphernalia into Dejima. He hears the voice of Jesus, who assures him that rather than remaining silent as Rodrigues had thought, Jesus also suffered alongside those who were killed.

Despite having apostatized, Rodrigues is forced by shogunate officials to prove that he is not practicing his former religion in secret. Kichijiro is arrested after being caught with a Christian amulet and Rodrigues never sees him again. The former priest lives out the remainder of his life in Japan. After his death in 1685, he is given a traditional Japanese funeral. His wife is allowed to place an offering in his hand to ward off evil spirits - she places the tiny crudely made crucifix that was given to him when he first came to Tomogi, indicating that in his heart, Rodrigues remained a Christian all his life.