Only in the real world do humans possess free will, whereas any film about the nature of belief effectively requires the director to play God, forcing them to answer the very questions they often set out to raise. Despite this paradox, in the history of cinema, there have been many great films about Christian faith — though not nearly enough: Carl Theodor Dreyer’s “Ordet,” Robert Bresson’s “The Diary of a Country Priest,” Jean-Pierre Melville’s “Léon Morin, Priest.” Now, add to that Martin Scorsese’s “Silence,” which marks the culmination of a nearly 30-year journey to adapt Japanese novelist Shūsaku Endō’s tale of a 17th-century Jesuit missionary faced with the dilemma of whether to apostatize.

And yet, judged in broadly cinematic terms, “Silence” is not a great movie, despite having been directed by one of the medium’s greatest masters at a point of great maturity (this is the last film one might expect to immediately follow the bacchanalian excess of “The Wolf of Wall Street”). Though undeniably gorgeous, it is punishingly long, frequently boring, and woefully unengaging at some of its most critical moments. It is too subdued for Scorsese-philes, too violent for the most devout, and too abstruse for the great many moviegoers who such an expensive undertaking hopes to attract (which no doubt explains why Scorsese was compelled to cast “The Amazing Spider-Man” actor Andrew Garfield and two “Star Wars” stars).

Still, viewed through the narrow prism of films about faith, “Silence” is a remarkable achievement, tackling as it does a number of Big Questions in a medium that, owing to its commercial nature, so often shies away from Christianity altogether. Considering the dominant role religious belief plays in the lives of so many, it’s surprising, even scandalous, that so few films face the subject head-on. “Silence” is the largest, most serious-minded examination of faith since Terrence Malick’s “The Tree of Life,” rounding out a trilogy on the subject from the director of “Kundun” and “The Last Temptation of Christ.”

At the core of “Silence” lies the dilemma: What does it mean to apostatize? Though the screenplay (which Scorsese adapted with Jay Cocks, his collaborator on “The Age of Innocence” and “Gangs of New York”) intends for us to consider this question on some deep teleological level, the film would do well to engage with it first in more literal terms. For those not already versed in the finer points of Christian dogma, “apostasy” is the act by which someone renounces his faith, represented in the particular context of this film by placing one’s foot upon a fumi-e (or religious carving of Mary or Jesus). Here, apostasy is the weapon by which 17th-century Japanese officials, threatened by European colonial powers and the missionary faith they brought with them, sought to combat the spread of Christianity among peasants receptive to the notion that their suffering might be lifted in heaven.

In Scorsese’s comparably low-key “Kundun,” the future Dalai Lama learns the Four Noble Truths of Buddhist teaching. “What are the causes of suffering?” his teacher asks, to which his pupil responds, “Pride. Pride causes suffering.” This is a priceless insight, and one that Garfield’s character, a presumptuous young “padre” named Sebastião Rodrigues, might do well to learn. Though Rodrigues imagines his greatest obstacle to be God’s silence (he prays constantly, and yet He never responds), the story hinges on the character’s seemingly unbreakable arrogance — a dimension significantly downplayed in Garfield’s self-effacing performance. Instead, the actor focuses on Rodrigues’ doubt, as reflected in the dense clouds of fog and mist that permeate much of the film.

If “Apocalypse Now” was a modern twist on “Heart of Darkness,” then “Silence” could fairly be viewed as Scorsese’s own take on that paradigm. Call it “Soul of Murkiness.” Together with another Portuguese priest, Francisco Garrpe (Driver, who looks the part, his lean, angular face reflecting the severity of classic religious icons), Rodrigues petitions his Jesuit superior (Ciarán Hinds) to let them travel to Japan to investigate the fate of their mentor, father Cristóvão Ferreira (Liam Neeson) — who’s effectively the film’s AWOL Kurtz. Their only clue is a long-delayed letter, which tells of unspeakable torture practices visited upon Christian priests and converts alike in an attempt to discourage the spread of the religion, coupled with rumors that Ferreira ultimately apostatized and now lives with a wife as a Japanese.

For the sincerely devout Rodrigues, the mission represents an opportunity to do good, offering salvation to the savages, but also a shot at glory. He makes the journey — which, in a two-hour-and-41-minute movie, passes in the blink of an eye — in full awareness that he could be martyred for his actions. With martyrdom comes divine reward (including the possibility of special visions, a privileged place in heaven, and eventual sainthood), and in Endō’s novel at least, he yearns for the opportunity.

The reality that awaits Rodrigues and Garrpe is every bit as hellish as they had imagined, and then some, and Scorsese renders these scenes of torture — boiling water drizzled over exposed flesh, women wrapped in straw and set on fire — with the same unflinching detachment Pier Paolo Pasolini did the sadism of his infamous, incendiary final film, “Salò, or the 120 Days of Sodom.” And yet, Rodrigues persists, consciously risking his safety in order to locate and serve the “Kakure Kirishitan” (or “hidden Christians”), who have been forced underground by these terrible punishments, inquiring as to Ferreira’s whereabouts with each fresh encounter.

The first Japanese the missionaries encounter is a wily ex-Christian named Kichijiro (Yôsuke Kubozuka), whose sneaky, social-outcast behavior suggests the way Toshiro Mifune might play the role of Gollum. Kichijiro has apostatized once already, and he will again before the movie ends, repeatedly betraying his faith and returning to beg forgiveness. Generally speaking, the casting of the Japanese characters favors actors who look like ghoulish exaggerations — like the rude caricatures found in Tintin comics, their teeth and fingernails smeared in grime. Compared with the humanely depicted natives of Roland Joffe’s more conventionally accessible/satisfying “The Mission,” the Japanese here come across as frighteningly “other,” almost animalistic. An unnerving inquisitor named Inoue (Issey Ogata) has a wheedling voice and faux-gracious manner that suggests the Japanese equivalent of Christoph Waltz’s Nazi colonel in “Inglourious Basterds.”

This style of representation marks a troubling, but no doubt deliberate choice on Scorsese’s part — especially compared with Garfield’s bare-chested, fabulously coiffed Rodrigues. Underscoring where our sympathies are expected to lie, the missionary outsiders all speak English (with wildly varied Portuguese accents), while the comparably heathen locals communicate in subtitled Japanese. Unlike Endō’s own big-screen adaptation of his novel, filmed by Japanese director Masahiro Shinoda in 1971, here, the local becomes the “other” — especially since the second half of the film concerns the two priests’ captivity and the sadistic attempts to convince them that Japan is a “swamp” where their religion “does not take root.”

Rodrigues is prepared for martyrdom, but not for the Japanese inquisitor’s more diabolical scheme, which involves torturing other Christians until he apostatizes. Worse still, Rodrigues watches as his cohort achieves the martyrdom he seeks (in a horrific beachfront scene that rings strangely hollow). Through it all, Rodrigues continues his appeal to God, praying for guidance, but receiving only … silence. Until he doesn’t.

The film’s last hour is by far its most challenging, as Scorsese goes out of his way to avoid some of the sweeping, free-associative techniques Malick has innovated for spiritual cinema, turning instead to the austere model of Bresson, Dreyer, and others that “Last Temptation” screenwriter Paul Schrader once described as “transcendental cinema,” in which powerless protagonists struggle against forces beyond their control. Whereas Endō’s novel allows omniscient access to Rodrigues’ deep internal conflict, the film leaves audiences at arm’s length, forcing us to scrutinize Garfield’s face for psychological insights that, for most, are too complex to expect us to interpret on our own.

For non-believers in particular, when Neeson resurfaces, his arguments, intended as the cruelest temptation, will instead sound perfectly logical. What Ferreira describes as “the most powerful act of love that has ever been performed” feels like a no-brainer, with no catharsis to ease the anti-climax. From the Crusades to the Spanish Inquisition, when one considers all the cruelty that religion has exerted on the world, it seems almost unfair to focus on this footnote in world history, where priests were punished for their beliefs, the way early Christians were thrown to the lions.

And yet, these paradoxes surely aren’t lost on Scorsese, who has created a taxing film that will not only hold up to multiple viewings, but practically demands them. Here, as ever, he brings an arresting visual sense to the project, reteaming with production designer Dante Ferretti and DP Rodrigo Prieto to create evocative widescreen tableaux, shot on celluloid and shrouded in mist and shadow, while relaxing some of his flashier techniques (with its Peter Gabriel score and aggressive cutting, “Last Temptation” feels dated today in a way that the director clearly intends to avoid here). What little music “Silence” does contain is featured so faintly as to be almost subliminal, leaving ample room for engaged audiences to personalize the viewing experience, while frustrating those grasping for clues as to the precise emotional reaction Scorsese intends. That’s a risky move, as is the dramatic way he breaks the silence in the end. Those who put their faith in Scorsese may find it challenged as never before by his long-gestating passion project.