The film had been pilloried by conservative Christians for a dream sequence in which Christ has sex with Mary Magdalene. In depicting Christ’s life as a doubt-ridden struggle between his human and divine natures, Scorsese had intended to make a film that was at once an act of doubt and an act of faith. In the novel he was reading, the priest was shown profaning an image of Christ, and yet the act was an act of faith.

The train slid past the mountains. Scorsese turned the pages. This novel spoke to him. All at once he saw it as a picture he would like to make.

The novel was “Silence,” by Shusaku Endo, a Japanese convert steeped in European literature and the history of Catholicism in Japan. Published in Japan in 1966, “Silence” sold 800,000 copies, a huge number in that country. Endo was called “the Japanese Graham Greene” and was considered for the Nobel Prize. Greene referred to “Silence” as “one of the finest novels of our time.”

The Jesuit missionary Francis Xavier brought Catholicism to Japan in 1549. In the next century, it was suppressed through the torture of missionaries and their followers, who were forced to apostatize by stepping on the fumie — a piece of copper impressed with an image of Christ. In “Silence,” Endo took the missionaries’ point of view, casting much of the novel in the form of letters by Rodrigues reporting back to his superior. He goes to Japan with another young priest, Francisco Garrpe, vowing to seek the truth about their mentor, Father Cristóvão Ferreira, but they are captured and shown the dogma-defying reality of human suffering under torture. The shogunate invites the Japanese converts to avoid torture by stepping on the fumie. Many do; some are tortured anyway. Rodrigues sees converts crucified, burned alive, drowned. A magistrate fluent in Christianity makes a grim proposal: Rodrigues can save the lives of the converts under torture if only he will step on the fumie and apostatize.

When Scorsese returned from Japan, he procured the film rights to “Silence.” As the years passed, hardly a day went by without his mentioning the project to the people around him: actors, friends and even his old parish priest, Father Principe. As he made “The Aviator” and “The Departed,” “Shutter Island” and “Hugo,” he insisted that “Silence” was the picture he really wanted to make. A Jesuit was elected pope; Islamic terrorists began targeting Christians in the Middle East. In 2014, with “The Wolf of Wall Street” a hit, Scorsese declared that “Silence” would be his next picture: He wouldn’t commit to another until it was finished. Twenty-six years in, filming began.

What led this great American artist to make a story of missionaries in Japan his ultimate passion project? He is known for his gangster pictures; he is a grandmaster of the profane. From the beginning, he has revealed himself to be an artist of intensely Catholic preoccupations, and the poisoned arrow of religious conflict runs straight through his career. “Taxi Driver”: a Vietnam vet as a spiritual avenger, bent on cleansing the city of filth through violence. “Cape Fear”: a tattooed fundamentalist determined to exact God’s justice. “Kundun”: a young man raised to be a spiritual master, thrust up against spirit-killing communism. Even “Living in the Material World,” Scorsese’s documentary about George Harrison, takes as its theme the conflict between flesh and spirit, between Beatle and seeker.

“Silence” is a novel for our time: It locates, in the missionary past, so many of the religious matters that vex us in the postsecular present — the claims to universal truths in diverse societies, the conflict between a profession of faith and the expression of it, and the seeming silence of God while believers are drawn into violence on his behalf. As material for Scorsese, then, “Silence” is apt, and yet Scorsese’s commitment to it has been extraordinary, even by his exacting standards. To understand that commitment, I spoke with the filmmaker, with members of the cast and the production team and with others who know the novel well — trying to grasp just what kind of an act of faith this film is.