Whether this represents God’s vision or that of the priests, it is very much the point of view of the movie’s own creator. This overhead shot and others suggest that there’s a divine aspect to the priests’ mission, an idea that Mr. Scorsese visually and narratively underlines in the Lazarus-like cave in which Rodrigues and Garupe first take shelter in Japan; in Rodrigues’s self-aggrandizing identification with Jesus; and, crucially, through the figure of Judas. As in Mr. Scorsese’s 1988 film, “The Last Temptation of Christ,” his messy, excitingly alive adaptation of that Nikos Kazantzakis novel, Judas must play a part in “Silence” because without him there can be no Jesus.

Once in Japan, Rodrigues and Garupe make contact with a village of hidden Christians, who live in fear of the authorities and a cobralike smiler known as the Inquisitor, Inoue (Issey Ogata, in one of the film’s strongest performances). By day, the priests hide in a small, cramped hut near the village; by night, they lead their new flock in dimly lighted rooms, delivering sermons in Latin, baptizing children and taking confession. Mr. Scorsese draws some modest, uneasy comedy from the linguistic and cultural differences between the priests and their congregation, as when a grabby, highly agitated woman begs the rather startled Garupe to hear her confession.

Despite the mugging from both confessor and confessed, the exchange feels forced and comes across as a bid to lighten the gloom; if anything, it turns a feverish plea for absolution into a bit of vaudeville. There’s something uncomfortably and literally childlike about this child of God, who, like the other villagers, with their pleading eyes and hands, seems like a relic from a white-savior myth. Kichijiro, who enters grunting and twitching, as if in homage to Toshiro Mifune, and grovels at the priest’s feet, also seems on hand as much for comic relief as for guidance. Yet, even as the film seems to share the outsider perspectives of Rodrigues and Garupe, instructively, it is the village elders — brilliantly played by Yoshi Oida and Shinya Tsukamoto — who give these scenes flesh, bone and pain.

“Silence” is based on the 1966 novel by the Japanese author Shusaku Endo that has attracted heavyweight admirers since it was first published. Graham Greene praised the novel, as did John Updike; for years, Mr. Scorsese tried to turn it into a film. (He wrote the foreword for a recent edition.) Filled with reams of religious dialogue, the novel fictionalizes history — the 17th-century purging of Christianity in Japan — as a means to explore religious faith and cultural difference. What preoccupies Endo is whether Western Christianity can take root in what the Inquisitor describes as “this swamp of Japan,” which seems inhospitable to outside forces. It’s a story of God, nation and myth.

It’s easy to understand Mr. Scorsese’s interest in the novel and specifically in the character of Rodrigues. Despite the priest’s piety, black vestments and narrative prominence, he is no more a Hollywood hero than most of Mr. Scorsese’s falling and fallen men, with their arrogance and vanity. Rodrigues cowers in fear, recoils from his flock and assures himself of the goodness that the church — and he, by extension — has brought. (He pities the worshipers but is proud of his ministering.) His faith, including in himself, sustains Rodrigues, but even as he tends to the souls of the hidden Christians he fails to ease their earthly suffering. God is silent; in a way, so is this most ardent missionary.