One of the challenges of turning the Noah story into a film is that the only conflict in the Biblical narrative is, implicitly, between Noah and God (whose impossible demands Bill Cosby famously answered with “Right. . . . What’s a cubit?”). Aronofsky was more interested in the tribulations that the Bible elides: the anguish of all the people denied room on the ark. What if one of them did get aboard—and then tried to thwart Noah’s plan? To deepen this tension, he and Handel played up the Biblical division of man into two teams: the descendants of Cain (wicked) and the descendants of Seth, including Noah’s family (righteous).

Just after soaking Russell Crowe, Aronofsky turned to submerging Tubal-Cain, a minor Biblical figure whom he and Handel had turned into Noah’s adversary. A warlord who murdered Noah’s father, Tubal-Cain combines brutality and wounded bewilderment: why does God speak to Noah but not to him? He’s played by Ray Winstone, a British character actor who is a master of the endearing thug. “Where Russell is an aikido opponent—you have to accept the force coming at you and work with it—Ray is a fun sparring partner,” Aronofsky said. He put his arm around Winstone and explained the scene: Tubal-Cain is climbing the ark with an axe, trying to hack his way in, when the flood hits. “It’s going to be ‘Oh, shit, here comes the wave!’ And then we’re going to dump a whole fucking lot of water on you, and you look around, amazed—this is the end of the fucking world!—and keep chopping.”

“When you want amazement or awe, it helps to silently work your lips,” Winstone said, his words a Cockney blur. “I say ‘cunnilingus.’ ”

“Beautiful!” Aronofsky said. After watching a take on his handheld monitor, he added an air mortar to the six buckets of water, so the actor would have to struggle to stay upright. Winstone, who got sunstroke and lost movement in his right arm during the filming, later told me, “I think Darren takes great pleasure in seeing you go through pain—you go again and again and again. He pushes you to the limit, looking for perfection.”

After watching several more takes, Aronofsky told Matthew Libatique, the cinematographer, to get even closer. In dramatic moments, the director brings the lens in extremely tight. (Ellen Burstyn, the star of his second film, “Requiem for a Dream,” told me, “I’ve never had anybody strap the camera on me before.”) Aronofsky said, “The best invention of the twentieth century was the closeup. That you could put a camera right in front of Paul Newman’s eyes and look into his soul changed storytelling.” Once Aronofsky is in close, he turns the camera around to put us into his characters’ heads. Since they’re scrabbling to get out of them, this is a disturbing place to be. “Darren can portray the inner mind better than almost anybody,” the studio head Harvey Weinstein said. “Whatever that character is feeling—the emptiness, the obsessiveness, the nightmarish—he gets it into your head.”

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When Aronofsky screened “Requiem for a Dream”—a scarifying portrait of four addicts—at Cannes, in 2000, the audience’s prolonged discomfort swelled into catharsis. One of his executive producers, Nick Wechsler, began laughing hysterically during the film’s assaultive final barrage, which intercuts among the main characters as Harry has a gangrenous arm amputated, Ty is brutalized on a chain gang, Marion labors in a sex show to feed her heroin habit, and Sara convulses from electroshocks in a psych ward. When Aronofsky asked what Wechsler was laughing at, he pointed at the crowd: “Look what you’re doing to those people!” The French audience rose for an ovation that lasted fifteen minutes, overcome by the film and delighted that they’d never have to see it again.

At the Armory, Aronofsky watched as Winstone practiced steeling his jaw. “Maybe it’s two things,” he suggested. “Disbelief at what’s coming, and then defiance.” “Fuck you, you motherfucking cunt, giving me two seconds to do all ’at,” Winstone said. “I know you will amaze me,” Aronofsky said, radiating belief. Cradling his monitor, he crept so close that he was almost in the frame. When the flood hit Winstone, Aronofsky’s knees buckled, and then he surged up in unison with the actor, fighting back to life.

Aronofsky told me, “The closest I get to the unconscious is between ‘Action!’ and ‘Cut!’ When the actor is in the Michael Jordan zone, dunking high above the rim in super-high resolution, I become aware of what the camera is shooting without seeing my screen—I’m in the movie, feeling what the audience will feel.” He laughed. “And then, after ‘Cut!,’ the reality of limited time and money floods back, and I think, Fuck, can I get another hit before I’ve got to leave?”

Aronofsky writes his films on the second floor of his place in Manhattan’s East Village, at a custom-built desk of Bastogne walnut, inlaid with responsibly harvested macassar ebony and pink ivory. Twenty-five puzzles are concealed within it, cunning locks and springs and slides, and the front houses an octave of organ pipes you can play by sliding drawers in and out. As you solve the puzzles, you find hidden pieces of wood, each of which displays a few musical notes. When you put the pieces in order and play the resulting tune on the organ—an Irving Berlin song that was the first thing Aronofsky learned on the piano—it opens a secret safe: the final prize. It took him six weeks to pop the safe, and he had the plans. David Blaine told me, “The desk is a very cool thing that’s a lot like Darren himself—there’s always another twist and turn.”

Aronofsky enjoys the all-access life: introducing a speech by the Dalai Lama, or having his friend Patti Smith write a lullaby for Russell Crowe to sing in “Noah.” (Smith said she was so determined to meet Aronofsky’s expectations that “I wrote like a hundred versions of this tiny little song.”) But at his fortieth-birthday party the only celebrity present was the actress Rachel Weisz, who was then his fiancée. The room was filled by the friends he played Chinese handball with as a boy in Brooklyn’s Manhattan Beach—a lawyer, a bar owner, and a gastroenterologist—and by members of his longtime production team, most of them friends from his college years at Harvard or from the American Film Institute, where he studied directing in the early nineties. (In an unconscious gesture of solidarity, Aronofsky’s team often adopts his current hair style—recently a shaved head and a thick beard—as if someone were mass-grooming them using the magnetic Wooly Willy game.) “His films are all about one character who’s very isolated—and that’s the opposite of Darren,” Ari Zablozki, the bar owner from the Manhattan Beach posse, said. “He needs people, interactions.”

When Aronofsky interviewed the famously low-key Clint Eastwood for the Tribeca Film Festival, last year, he said, “You make it seem so easy—and for me filmmaking is pain. I’m in pain the whole time. I’m in pain writing, I’m in pain shooting, and I’m in pain editing, and I just—how do you do it?” Eastwood drawled, “If it was that painful, I would consider myself somewhat of a masochist.” Away from the set, though, Aronofsky can experience a kind of withdrawal. In 1996, he wrote in his diary about going to a rave in Thailand: “The tide came in, the sun came up, everyone kept dancing; the tide went out, the sun went down, everyone kept dancing. I was miserable because I wasn’t making films.” Many of Aronofsky’s characters seek to escape themselves through drugs, either dulling the pain or opening the doors of perception. (In the new film, Noah’s vision of the ark is inspired by psychedelic tea.) When Nina, the rigid ballerina played by Natalie Portman in “Black Swan,” finally loosens up after rolling on Ecstasy, the camerawork, too, strobes and skips and melts, and we’re briefly having fun. “Darren’s not a druggie at all—he’s a nice Jewish boy from Brooklyn,” Portman told me. “But he wanted me to try it before doing the scene. I said, ‘Just tell me what it’s like!’ ” So he did. When I mentioned Portman’s recollections to Aronofsky, he assumed an expression of exaggerated rectitude. “I would never encourage Natalie to do drugs,” he said. “Write that down. I think Google is an incredible research resource. C’mon, write that down.”

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Harvey Weinstein said that, on the basis of Aronofsky’s films, “you’d expect him to be living in an attic with a door that someone shoves food under. But when he’s not making a film Darren is the kind of guy—so much fun, with a great, hearty laugh—you’d go out for a beer with and talk about kids, girls, anything but psychological obsessions.” On a recent vacation in Mexico, the director hid a rubber lizard under his older sister Patti’s pillow. After she screamed, Aronofsky cried, “That makes up for the butter!” Forty years earlier, Patti had told him to open his mouth and close his eyes—then placed a pat of butter on his tongue. He never ate butter again, and is now a semi-vegan. When he must drive, he drives a Prius, an unusual model painted Habanero orange, but much of the time he navigates the city on a scooter. It keeps people off balance: “You’re not a skateboarder, you’re not a biker, you’re not an asshole—they don’t know how to deal with it.”