The film unfolds in 1633, beginning with a chilling prologue where the young Portuguese Jesuit priest, Cristóvão Ferreira, witnesses the horrific torture of Japanese converts he's been striving to convert to Christianity. Despite his presence, he feels utterly powerless against the Japanese authorities conducting these brutal acts.
As years pass, at St. Paul's College in Macau, an Italian Jesuit priest, Alessandro Valignano, receives alarming news indicating that Ferreira has renounced his faith (apostasy) under the duress of torture in Japan. His Portuguese pupils, Jesuit priests Sebastião Rodrigues and Francisco Garupe, driven by disbelief and a desire to rescue Ferreira, set off on a perilous journey to uncover the truth. They are joined by Kichijiro, an alcoholic fisherman who fled Japan to save himself, willing to guide them back.
Upon their arrival in Japan, specifically in the village of Tomogi, the priests are disheartened to discover that the local Christian communities have been forced underground. Their shock intensifies when they witness a samurai, referred to as the "Inquisitor," mercilessly torturing villagers by strapping them to wooden crosses at the ocean's edge, where rising tides ultimately claim their lives. The subsequent cremation of bodies on a funeral pyre deeply troubles the priests, who recognize it as an act meant to thwart Christian burials.
Believing their presence might trigger further terror from the shogunate, Garupe decides to head to Hirado Island, while Rodrigues ventures to Goto Island—the last known residence of Ferreira—only to find it ravaged and desolate. As Rodrigues roams through Goto, he grapples with a harrowing moral dilemma: whether resisting the demand to recant is egotistical when it could alleviate the suffering of others. His journey leads him to a fateful reunion with Kichijiro, who betrays him to the samurai.
Taken prisoner and transported to Nagasaki, Rodrigues finds himself among many other captured Christians. During a tribunal, he's informed that Catholic beliefs are categorically opposed in Japan. He insists on meeting Governor Inoue Masashige (Issei Ogata), who unexpectedly turns out to be the elderly man presiding over his case. After being imprisoned again, Kichijiro is brought in and admits that he was coerced into turning him in. He asks Rodrigues for absolution for his betrayal, which Rodrigues reluctantly grants. Upon being instructed to step on a Fumi-e (a crude depiction of a crucifix), symbolizing his rejection of Christianity, Rodrigues abandons his faith to escape further torment.
In a tragic twist, he later observes Garupe and other prisoners being led to the shore, where they are fated to drown unless Garupe renounces his faith. Although still restrained, Rodrigues witnesses Garupe’s unwavering resolve, and tragically, Garupe is drowned while attempting to save another prisoner.
Eventually, Rodrigues meets the older Ferreira, who reveals that he too abandoned his faith under torture, concluding that Christianity in Japan is futile. Rodrigues vehemently rejects Ferreira's despairing views, yet later, as he hears the agonizing cries of Christians in suffering, an inner voice of Christ compels him to forsake his convictions, leading him to step on the Fumi-e.
Years later, after Ferreira’s death, Kichijiro approaches Rodrigues once more, asking for absolution, yet Rodrigues declines, declaring his withdrawal from the priesthood. Kichijiro, later apprehended with a pouch containing a religious amulet he denies ownership of, disappears, his fate remaining unknown. Ultimately, Rodrigues passes away, and his body is cremated, holding in hand the tiny crucifix given to him upon his arrival in Japan.
