Martin Scorsese’s career is built on stacks of films that have looked at the good and bad sides of humanity. The battle between these areas has been the fodder for works from “The Last Temptation of Christ” to “The Wolf of Wall Street.”

The spiritual elements of such conflicts have been masked by the director, who has been more intent to look at how people react to clashing morality questions rather than pondering the questions themselves.

That changes with “Silence,” Scorsese’s adaptation of Shusaku Endo’s 1966 novel about the story of two Jesuit missionaries — Father Rodrigues (Andrew Garfield) and Father Garrpe (Adam Driver) — go to 17th century Japan in search of their mentor, Father Ferreira (Liam Neeson). What they find is a persecution against their Christian thinking that tests their faith.

Before the missionaries can start their search, they find the horrible torments that are being done to any Japanese who have changed to a Christian belief. Despite an ever present reality their thinking could result in their death, the believers continue to practice their faith. The arrival of the missionaries is seen as a sign.

Chief among those looking to drive any Christian thinking out of the country are inquisitor Inoue (Issei Ogata) and his translator (Tadanobu Asano). Inoue uses his time with Father Rodrigues as a way to not only eliminate one more spark of Christianity but also to send a major message that anyone who continues to practice their faith will be tortured or killed.

There is no denying that the director embraces the chance to present arguments about faith, will power, bigotry, hatred and the use of religion as a tool to generate fear and self doubt. He presents all of these views with deep passion, particularly in scenes where Father Rodrigues goes from a intense defense of his belief to a soul-searching reality that he has some doubts.

All of this is presented against a massive backdrop that harkens back to the days when director David Lean was making epics like “A Passage to India.” The beautiful setting creates a harsh contrast to the spiritual ugliness.

Scorsese’s passion for the project blinded him on occasion. Maybe it’s the fact that Garfield’s latest work had him playing another character of divine faith with “Hacksaw Ridge.” Whatever the case, there are moments when he goes from playing a character to sounding more like a carnival barker.

For some very odd reason, the characters of Inoue and his translator come across more like escapees from a junior high production of “The Mikado” than as the serious pillars of this battle of faiths. This is a very serious story of what happens when two people who are equally passionate about their religion come together. A more somber approach to the performance would have been better.

When a film has established its credential so deeply, small moments can be distractions but not diversions. The majority of “Silence” is a deeply moving story of faith, where unlike most movies in the genre, there are no clear answers.

Scorsese merely offers up two powerful perspectives and drives them into each other. That kind of collision often generates a new set of questions by those looking in from the outside.