Talking with Thelma Schoonmaker recently, it became quickly apparent that I wasn’t even going to scratch the surface of her career’s work with Martin Scorsese in a single piece. I couldn’t help but play the retrospective game with her, and while I of course didn’t address all 19 feature collaborations, I was curious about six films in particular that I think represent a nice cross-section of their work together. Each of them – “Who’s That Knocking At My Door,” “Raging Bull,” “The Last Temptation of Christ,” “Goodfellas,” “Bringing Out the Dead” and “The Departed” – will get its own space in the next few days.

While Academy members may be tongue-lashing Martin Scorsese for the near-NC-17 nature of his latest film, “The Last Temptation of Christ” remains, unequivocally, his most controversial work to date. An adaptation of the Nikos Kazantzakis novel that surmised a Jesus more human than divine, it was predictably burned in metaphorical effigy upon release in August of 1988.

Not so metaphorical, however, was the actual burning of the Saint Michel theater in Paris with Molotov cocktails by lunatics who severely injured a number of people during a showing of the film. Director Franco Zeffirelli, rather than support the daring of a fellow artist, withdrew his film “Young Toscanini” from the Venice Film Festival when “Last Temptation” was scheduled for the program that year, and some theater chains even refused to screen it due to the uproar.

But before all of that controversy, in her New York editing suite, watching the dailies come in from Morocco, Thelma Schoonmaker wasn’t outraged. She was moved to tears.

“The footage wasn’t even developed yet because there were no labs over there at that point,” she recalls. “At least on ‘Kundun’ it wasn’t quite so bad, also shot in Morocco. But it was quite moving for me because the landscape of Morocco, just the red of the soil, seemed to be about the blood of Christ that is so important in the movie. I started crying in dailies. That hardly ever happens.”

Scorsese was having trouble reaching his editor by phone in those days from his location shoot, eager to know whether he was getting what he needed or not. When he finally got through, Schoonmaker just broke down and wept. “I couldn’t talk to him about it,” she confides. “He said, ‘Well, what’s the matter? Is it ruined?’ And I just kept saying, ‘It’s so moving! It’s so moving!’ And I wasn’t the only person crying in dailies; his development person was also crying. Finally I said, ‘No, no it’s very beautiful.'”

When you look across Scorsese’s filmography (and as noted briefly in yesterday’s “Bringing Out the Dead” piece), religion is a huge part of his work. It goes all the way back to his very first feature, statues of the Virgin Mary permeating the imagery of 1967’s “Who’s That Knocking At My Door.” It’s very clearly something he meditates on as an artist, and it made him the perfect, if in some ways unexpected, candidate to capture Kazantzakis’ thoughtful narrative on film. Alas, that deep-seeded sense of faith and divine consideration was lost on the ignorant.

“It’s such a religious movie,” Schoonmaker says. “And then we were attacked by the fundamentalists. We begged them to come see the movie. Everybody else came. Catholics, Episcopalians, the Bishop of New York supported us completely – the Episcopalian Bishop of New York. But the fundamentalists would not come. We had to have bodyguards for Marty. It was terrible. And we had to rush the movie out to defend itself. Then, you know, it just sort of died.”

Musician Peter Gabriel provided the ethnically influenced original score for the film, and according to Schoonmaker, was incredibly devoted to the process. “He came to New York and he had a studio on the floor below us,” she recalls. “We would go down, Marty and me, and there would be some Indian double electronic violinist playing and Peter singing. He kept re-scoring as we cut the movie down. We said, ‘No, no, no, you have to wait until the end and then score it.’ He was still making changes on the last day we were mixing the sound! But he was wonderful. What a score that is.”

While the release of the film was a difficult experience, the actual production itself was no picnic either. “He had five stuntmen from Italy and they had to play the Romans and the Jews,” Schoonmaker explains. “So he would shoot, first, the Jews jumping down and then he would change them into the Romans. It was horrendous. And when they shot the crucifixion, there were weather problems and wild dogs running around. The guys who were playing the thieves were dancers from Casablanca and they were so grateful to have the part that they kept throwing kisses to Marty as he was trying to shoot the movie. And then they almost didn’t get it because the sun was going down. It was a nightmare.”

But they did get it, and the result was a Best Director Oscar nomination for Scorsese (though nothing else for the film) that Schoonmaker doesn’t even remember today. Perhaps the fog of strife surrounding the movie is too thick in her memory all these years later. But regardless of laurels and trophies, “The Last Temptation of Christ” is one of the most penetrating depictions of faith’s profound and unavoidable foil: doubt. It’s about the yin and yang that the devout understand, whether they want to embrace it or not. And clearly, many weren’t able to embrace it or even consider it here, how moving the idea really is. Of course, I write that as someone without such religious devotion, but as someone who nevertheless finds great power in such poetry.

“Marty just wanted to show that Christ was human and, you know, didn’t want the job,” Schoonmaker says. “I think that’s such a beautiful idea. ‘Not me! No, no, no! Get somebody else!’ And that wonderful moment when he says to Judas, ‘I’m gonna have to die’ – what a realization. It was just a wonderful experience, to watch it all evolve.”

Don’t forget to read our longer interview with Schoonmaker about “The Wolf of Wall Street” and its place in the grander scheme of her career’s work with Scorsese.

“The Wolf of Wall Street” is now playing in theaters everywhere.