That last conundrum animates “Silence,” which I suspect is part of the reason I found myself resisting both Shusaku Endo’s novel and Martin Scorsese’s gorgeous adaptation of the book, which arrives in theaters this weekend.

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“Silence” follows two young Portuguese priests, Rodrigues (Andrew Garfield) and Garrpe (Adam Driver) — I suspect the movie might have been somewhat stronger if those two casting decisions were reversed — who travel to Japan in hopes of finding their mentor, Ferreira (Liam Neeson), who has fallen out of touch and who is rumored to have apostatized, disgracing himself and the church. With help from Kichijiro (Yosuke Kubozuka), who apostatized to save himself only to see his whole family murdered, Rodrigues and Garrpe begin to minister to a group of secret Christians led by Ichizo (Yoshi Oida) and Mokichi (Shin’ya Tsukamoto). Eventually, their renewed missionary work comes to the attention of Inoue (Issei Ogata), the inquisitor charged with stamping out Christianity in Japan. Though Inoue began his mission by executing huge numbers of Christian converts, he has decided that it is more effective to damage the credibility of Catholic priests, and he sets out to systematically degrade Rodrigues’s faith.

When Rodrigues leaves Macao for Japan, he is certain that his faith functions as a manual for the right decision to make in any circumstances. When he meets the drunken, damaged Kichijiro, Rodrigues overcomes his distaste and distrust to follow the man. When he meets Japanese Christians, he ministers to them, and when men come from the island of Goto on bleeding feet to beg for his ministry, Rodrigues goes, no matter the personal risk. He squares himself to withstand torture and finds the reports of Ferreira’s fall incomprehensible because he is sure that his spiritual teacher would have chosen martyrdom over apostasy.

But in what Inoue describes as “the swamp of Japan,” Rodrigues finds that this decision tree has been fatally corrupted. The first sign that Japan has changed him comes when Inoue arrives at the little community and tells the villagers to choose between stepping on an image of Christ and offering up hostages to be executed. Without him really being aware of it, Rodrigues’s fondness for his parishioners has gotten in the way. Without thinking, he tells them to apostatize, shocking Garrpe. It turns out that it’s easier to image sacrificing yourself for high principle than to ask others to do it.

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This is Inoue’s central, cruel insight. He crucifies men in the sea, beheads them in front of Rodrigues and hangs Japanese Christians upside down in pits of excrement. Rather than giving Rodrigues the opportunity for martyrdom the young priest had prepared for, Inoue asks Rodrigues what he would have others do to preserve their own purity, and his. And he and his interpreter (Tadanobu Asano) do so with a smiling malevolence and repeated expressions of concern for Rodrigues’s welfare that only emphasize the ingenious cruelty of their decision not to allow Rodrigues to suffer physical pain.

The final third of the movie essentially consists of a religious disputation between Rodrigues and his persecutors, which I think is intended to be staged in a dissatisfying fashion. Inoue insists that Christianity can’t survive in Japan and refuses to respond to Rodrigues’s insistence that persecution is the real problem. Another interlocutor tells Rodrigues that the Christianity his parishioners believed in is distorted, an amalgamation of sun-worship and veneration of the priests themselves. There are, in the mis-translations and misunderstandings that show up frequently in the early going in the movie, hints that this is true, but the question is never resolved.

Rodrigues is worn down by prison and eroded by the horrors he has witnessed. And even if he weren’t, the ongoing torture of other Christians lingers in the background of every argument like a frequency set to drive him, and us, to madness. This is not a debate that Rodrigues can win, or even clarify. It’s not even a conversation that truly helps him determine the best of a bad set of options. A debate would be something that could be resolved, a contest from which a hero could emerge, and disabusing us of the notion that this will happen is part of the point that “Silence” seems to be making. People frequently emerge from mist and water and foliage in “Silence,” but they disappear into them, too.

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This is not, as you might expect, entirely comfortable mental territory to occupy, especially at this moment in American politics and public life. “Silence” is not, of course, remotely intended as a meditation on Donald Trump’s impending inauguration as president of the United States; Endo published his novel in 1966, Scorsese first read it in 1989, and both book and movie are resolutely about Japan and Catholicism.

But just because not everything is — as some publications spent much of last year suggesting — a sign or a portent directly related to our current politics doesn’t mean the dread and confusion of “Silence” don’t resonate. Though our straits are far less severe, I, and many of my fellow Americans, seem to have wandered into a dark wood, and it’s not at all clear that anyone like Dante’s Virgil in “The Divine Comedy” or Christian’s Help from “The Pilgrim’s Progress” is coming to guide us in the right direction. I don’t know if it’s comforting or a cause for despair to think that in moments of darkness past, people have made the best of the awful decisions on offer and turned from public outreach to the preservation of their private souls.