Over darkness, environmental sounds (crickets chirping, etc.) turn to silence in sync with the title card.On a mountainside, Japanese men are being tortured by other Japanese men as Father Ferreira (Liam Neeson) watches and narrates. Their naked bodies are burned with boiling water from a hot springs, using ladles with holes so that the water spreads and the torture is more painful. They are then nailed to wooden posts. But Father Ferreira says some of the men were happy to die this way because they were being persecuted for being Christians in 17th century feudal Japan and they were happy to become martyrs to show how strong their beliefs are.A title card reads that the year is 1637. Two Portuguese Jesuits, Father Rodrigues (Andrew Garfield) and Father Garupe (Adam Driver) listen as Father Valignano (CiarÃ¡n Hinds) reads the letter, which is said to be the last known writing from their mentor, Father Ferreira. Valignano says that Ferreira eventually apostatized to avoid being tortured and now lives in Japan in an arranged marriage. The two Portuguese priests do not believe this because Father Ferreira was a huge believer of Christianity and a powerful influence on everyone he knew. They were going to be dispatched to find Ferreira, but with this message, the task seems complete. However, Rodrigues and Garupe beg permission to go to Japan to find out the truth about Father Ferreira and clear his name. Valignano reluctantly allows them to go.Christians are no longer allowed into Japan because of all the torture going on, spearheaded by a government official, the Inquisitor named Inoue (Issei Ogata). The two priests are taken to a Chinese boat which they'll use to be transported to Japan, under the guide of a Japanese man named Kichijiro (YÃ´suke Kubozuka), whom they find drunk and ragged on the floor of the boat. He promises to lead them to the Christians that are hidden although he claims he is not a Christian himself. On the voyage, the priests overhear Kichijiro muttering a prayer. But when asked, he still denies being Christian.The trio eventually makes it to Japan. Kichijiro seeks out Christians in the village and returns with a group who leads the two priests to a safe house. They continue up a mountain until they reach a charcoal hut in Tomogi, near Nagasaki. The priests are told to stay hidden inside. If any of the Christians want them to emerge, they will use a special knock. If someone approaches without knocking in the same fashion, the priests should immediately hide in a secret room built under the floorboards.Rodrigues and Garupe prove very essential to all the Christians who have had to live for years without a priest. The Japanese Christians confess to the men who are glad to offer their guidance despite not speaking the language and rarely being able to decipher what they are saying. Since the Christians aren't allowed to have anything that represents Christianity, Rodrigues gives them a crucifix that he has made himself. And he tears apart his rosary so he can give them each a bead. Kichijiro refuses to accept. He later explains that he WAS a Christian but, when his family was tortured, he denounced his faith. We see in a flashback Kichijiro's family held hostage after being declared Christians. One by one, they refuse to step on the fumi-e (a representation of Jesus) which later leads to them being burnt at the stake, but Kichijiro does trample on it, denouncing his faith to avoid death. This reveals why he doesn't consider himself a Christian.The two missionaries stay hidden in the tiny hut for a long period of time. They finally get restless and decide to go outside, despite the danger. After a time, they notice a few people watching from the bottom of the hill. Rodrigues and Garupe rush back into the hut and hide under the floorboard. Eventually they hear someone at the door, calling for them. The visitors sound like they want guidance but Garupe reminds Rodrigues they can't answer the door for anyone who doesn't signal as pre-established. Still Rodrigues trusts the men and emerges from the hiding spot. He learns that the group that has spotted them are Christians who had heard they were in the valley and traveled to request guidance. Their village, Goto, has kept their Christian beliefs because authorities have not yet persecuted them.Rodrigues becomes the priest for Goto and is happy to listen to confessions and hold masses. He is content with his work as a priest for the persecuted Japanese. But upon returning to Tomogi, he learns that a samurai and his men have been informed that there are secret Christians there and thus he will return to take hostages until the villagers agree to betray the Christians. He selects one man and tells the villagers to supply three more. Two leading Christians volunteer, and the villagers convince Kichijiro to be the third hostage since he is not from the village and thus won't be persecuted as harshly. Kichijiro reluctantly agrees. The men ask Rodrigues what to do if they're asking to trample the fumi-e. Rodrigues tells them to trample.The hostages are brought before a magistrate and told to trample on the fumi-e. They do so, as Rodrigues advised. But then they are ordered to spit on the fumi-e and to declare that the Blessed Virgin is a whore. The village men don't do this, but Kichijiro is quick to be blasphemous. He is set free while the other men are sent off to be tortured. They are put on crosses in the sea and when the high tide comes, they are slowly drowned. Rodrigues begins to have a crisis of faith, disappointed by the silence of God despite the agony of His followers.Rodrigues and Garupe separate. Rodrigues takes a boat to a new village but finds it abandoned, filled with filth and wild cats. He realizes that someone else is on the trail when he finds a fire that was recently put out. Eventually he finds Kichijiro who swears he was not the one who betrayed the villagers and hasn't betrayed Rodrigues, even though 300 silver coins are being promised for his capture. Kichijiro promises to take Rodrigues to a safe place. Rodrigues is reluctant to trust him but does so anyway.After Kichijiro gives Rodrigues salty fish to eat, he complains of thirst. Kichijiro leaves to gather water. When he returns, he drops the glass jar but tells Rodrigues that there is a stream nearby where he can drink as much as he would like. Rodrigues goes to the stream and looks at his reflection which turns into Jesus face, similar to his own ragged visage. He begins to laugh hysterically. And then realizes he is surrounded by officials. Kichijiro asks for forgiveness for his betrayal and silver coins are tossed at him by the persecutors.Rodrigues is taken to a village where some Japanese Christians are being held prisoner in a small hut. They give him some food and he begins to mentor the group. He is kept in his own small hut, a sort of prison made of wood. A samurai appears and tells the peasants their lives will all be spared if Rodrigues apostatizes.Rodrigues is brought before a samurai and they discuss Christianity. The man says the Japanese do not want Christianity. Rodrigues says that Christianity is not something that will only flourish in one area like plants, it can grow anywhere. The man points out that Japan is a swamp and plants cannot grow there. Rodrigues said it would grow if it the believers weren't being poisoned by persecutions and tortures. The man tells him the poison is Christianity. Rodrigues asks about Father Ferreira and is told he did, in fact, apostatize and now lives in Nagasaki with a Japanese wife in a home that was provided for him upon converting to Buddhism. Rodrigues demands to speak to the Inquisitor Inoue, the man who has spearheaded the cause to kill all Christians lest they apostatize. He learns that the man he's speaking to is the Inquisitor.Rodrigues is taken to a new prison where he meets other inmates, all Christians, whom he continues to mentor: preaching to them, hearing confessions. The other Christian prisoners are then brought out and told they have to trample on the fumi-e to apostatize. They're assured it's only a formality and it will not tarnish their beliefs to do so. All the men refuse to trample and are sent back to their prison, although one man is asked to stay behind. Rodrigues is relieved none of them were killed. Then a man approaches the remaining prisoner and quickly slices his head off. His headless body is dragged across the dirt, leaving a trail of blood, as Rodrigues and the other prisoners scream and cry. Once again, Rodrigues begins to doubt God because of His silence.Rodrigues debates with the Inquisitor about Christianity. Inoue says that if Japan had four concubines, should he persistently pursue the ugly ones? Rodrigues tells him Christians believe in monogamy which makes Inoue laugh. He admits that Christianity isn't necessarily evil but it has been used for evil and has ruined other nations. Rodrigues is returned to his hut and is treated well, which makes him suspicious.Rodrigues is taken to Nagasaki where he sees Garupe down on the beach, along with other Christians. These Christians are wrapped in straw mats and put onto a boat, which rows away from shore and then drops them into the sea. Rodrigues is told they all apostatized; he wonders why they they aren't set free. He is told the group are all peasant farmers and it doesn't matter what happens to them; what's more important is converting a priest to abandon his faith. Rodrigues tries to shout out that Garupe should apostatize to save the people's lives but he goes unheard. All the Christians are slowly drowned. Garupe swims out to them but also drowns. Rodrigues suggests being killed himself but is told they will not make a martyr of him.Rodrigues now lives in depression. Eventually he's taken to a Buddhist temple to meet someone. We flashback to a man being held upside down into a pit with his head blocked in by two wooden boards. This man is revealed to be Father Ferreira, now known as Sawano Chuan. Ferreira tells Rodrigues that he now writes on astronomy and medicine for the Japanese. He is also writing a book denouncing Christianity. Ferreira encourages Rodrigues to apostatize and tells him about the pit. We now see in full the method the Japanese used to torture Ferreira and convert him to Buddhism: a small incision was made behind his ear and then he was held upside down over a pit of feces as the blood slowly dripped down his head. He was kept there for days. He also tells Rodrigues that the Japanese Christians always had a distorted version of the religion. They've never accepted the God of Christianity. Rodrigues points out that he has seen many Japanese die for their beliefs. Ferreira tells him the Japanese have never had a concept of God and never will.Rodrigues will not apostatize and he is bound to a horse and paraded around the town. The townspeople berate him. He is encouraged to give up, being told that a lot of the hecklers were once Christians, now Buddhists. Rodrigues is taken to the Inquisitor's house and asked to denounce his faith to avoid torture, but Rodrigues refuses.Rodrigues is taken into a cell where he sees Laudate Eum carved into the wall. He spends the night worried about his impending torture. Kichijiro arrives and asks to be absolved for his sins. Reluctantly, Rodrigues does so. Father Ferreira arrives and tells Rodrigues that he was the one who carved Laudate Eum in to the wall because he was held captive there before being tortured in the pit. He tells Rodrigues that God was silent in his time of need.Rodrigues gets offended when he hears a loud snoring and screams that the guard stop being so loud on his fateful night. Ferreira tells him that the snores are actually the sounds of people being tortured and takes him nearby where he sees Japanese Christians hanging upside down in pits, as Ferreira had been. Rodrigues realizes he has been sitting by idly while this torture was going on, having mistaken the noise. Ferreira mentions the silence of God throughout Rodrigues' struggles and tells him that Christ would apostatize to keep the villagers from being tortured.The next morning, a fumi-e is brought out and Rodrigues is asked to trample on it. He struggles and then finally hears God's voice, telling him he was there throughout the silence, suffering alongside him. He hears Jesus telling him he must trample; that He was born into this world to share men's pain hence why He carried the cross. Rodrigues steps onto Jesus' figure and then collapses.Having apostatized, he is given the same fate as Ferreira. He is renamed Apostate Paul and spends his time, with Ferreira, checking trade goods and identifying any that have overt or hidden Christian symbols. One of the objects is the crucifix Rodrigues had initially given to a villager upon arriving in Japan.It is arranged for Rodrigues to take over the estate of a man after he dies, as well as the man's wife and a child. Rodrigues is regularly required to deny Christianity, in writing and in public by stepping on a fumi-e. At one such event, Kichijiro is found to have a religious emblem inside a necklace he wears. He says he acquired it from someone else and didn't know what was in its locket. He is dragged away.Forty years pass and Rodrigues spends the rest of his life in Japan as a Buddhist. He dies, and is given Buddhist rites. His body will be cremated as is the custom in Buddhism. But while his body is being burned, the camera reveals that a confiscated crucifix is clutched in his hand.