The Braintrust suggested a fix for the opening: why don’t we discover Mars through John Carter’s eyes, when he arrives? “That’s lazy thinking, guys,” Stanton replied. “If I do that, then thirty minutes in I’m going to have to stop the film to explain the war, and Dejah, and who everyone is, and we’re going to have even bigger problems.” Stanton is famously candid in other people’s Braintrust sessions, and famously prickly in his own. Lee Unkrich, who directed “Toy Story 3,” says, “Andrew is the guardian of the character of Woody,” the pull-string cowboy who wrangles the other toys. “Woody feels he has to lead and stubbornly adheres to his decisions, then has to untangle himself from the resulting mess—all qualities that are to some extent true of Andrew.”

Stanton and his writers came up with their own fresh opening: we briefly meet the warring Martian tribes in mid-battle and see the evil Zodangans receive a deadly nanofoam gun from the even worse Therns; only then do we cut to Earth and meet John Carter. But that was just the beginning of their attempt to overhaul a story that was already largely committed to film. Stanton storyboarded a group of new scenes and cut them into the film to convince Disney—or, as he put it, to “preëmptively prove”—that they would hugely improve the narrative. The studio acceded, and in April he began an unusually extensive (and expensive) eighteen-day reshoot.

One afternoon on the Playa Vista lot, Stanton was prepping a scene on the narrow ledge of a Thark temple. Carter and Dejah, who’d met earlier that day, warily agree to escape the Tharks and journey together to the shrine at the Gates of Iss, where Carter hopes to learn how to get home. The director listed the mistakes he’d made the first time. “The scene was matter-of-fact: if we light them pretty, you’ll think they like each other,” he said. “We didn’t take advantage of the small ledge for them to be intimate on. And we’d buried the lead—we hadn’t told you till later that Dejah was running from a forced marriage to her enemy, Sab Than, so she came across as unsympathetic. It’s my usual weakness, being too oblique. On ‘Finding Nemo,’ I originally had this whole slow reveal, in flashbacks, of the barracuda having eaten Nemo’s mother, which, as you never understood until the end why Marlin”—the father—“was so overprotective, made him totally annoying.” He shook his head. “It’s surreal how ‘The Taming of the Shrew’ can so easily become ‘Who’s Afraid of Virginia Woolf?’ ”

Taylor Kitsch lounged on the temple ledge, having his cordwood biceps misted with silicone spray, while Lynn Collins had her skim coat of tattoos and red shellac retouched. Stanton hovered alongside, as intimate as a pickpocket. He was following Steven Spielberg’s advice (“Get as close to the actors as you can”) and also his natural inclination. Kitsch can get broody, so Stanton strove to make their relationship feel like a two-buds-just-chilling hangout. The actor told me, “I fight with my director on every film, fight out of passion—but I never had a fight with Andrew, even on day eighty in the miserable fucking desert, because I respect him so much.”

Stanton playfully mashed up some dialogue from the scene, mimicking Kitsch’s sultry whisper and adding an overlay of the stoner drawl he himself used as the voice of Crush, the sea turtle in “Finding Nemo”: “What if I could take you to the gates, mon, and you were, like, ‘Earth, dude.’ ” After Kitsch laughed, Stanton waited a beat and casually added, “I need Sarkoja”—their Thark guard—“to have heard you for the next scene, so see if you can find a justification to speak a little more loudly.” Kitsch raised his intense murmur about two decibels, and the resulting take was both more casual and more sexually charged.

The following morning, the crew moved outdoors to reshoot the landing after Carter bounds into the sky to catch a falling Dejah, a move known on set as “the Superman catch.” Stanton directed his crane operators to shift a green-screen backdrop so he could capture the scene from a better angle, and told a stuntman to unspool the wire that dropped Carter and Dejah faster, then faster still. (Stanton later told me, “The conflict between safety and the collective belief of how superhero physics should work drove me nuts.”) He repeatedly moved a light-reflecting bounce card, trying to avoid irritating Collins’s eyes—she was blinking at just the wrong moment—and then had to wait half an hour for the sun to stop flaring off the camera lens. “Juggling weather and stunts and light and green screens—it’s like trying to do synchronized swimming with aircraft carriers,” he observed.

Still, he said, “This is what I wanted—after two decades in animation, I was spontaneity-starved.” And he couldn’t resist adding, “We came on this movie so intimidated: ‘Wow, we’re at the adult table!’ Three months in, I said to my producers, ‘Is it just me, or do we actually know how to do this better than live-action crews do?’ The crew were shocked that they couldn’t overwhelm me, but at Pixar I got used to having to think about everyone else’s problems months before all their pieces would come together, and I learned that I’m just better at communicating and distilling than other people.”

Sean Bailey, the president of production for Walt Disney Studios, was startled by Stanton’s “my kung fu is stronger than yours” approach, but he soon became an admirer. “Andrew is the opposite of the usual ‘We prep it, we shoot it,’ ” Bailey said. “He’s always dropping in new storyboards and scenes—it’s the Japanese idea of kaizen, a continual process of improvement. Any scene that’s an eight he’ll tear up to try to make a ten.”

Stanton’s home office, in Mill Valley, north of San Francisco, is a tidy, three-dimensional to-do list. Pinned to the crosspieces of his bookshelves are index-card reminders: “Inevitable but not predictable,” “Conflict + contradiction,” “How they choose is who they are,” and, in a different vein, “I don’t want success to follow me home.” It’s the office of a workaholic and a defender of the faith. Where Lasseter is Pixar’s beaming dad, Stanton is the noogie-dispensing firstborn who keeps his siblings in line. He once told Lee Unkrich, “I’m the older brother you never wanted.”

“I’d only known Andrew from Braintrust meetings when we started on ‘John Carter,’ ” Mark Andrews, who helped Stanton write the first drafts of the screenplay, says. “Friends who’d worked with him told me how collaborative he was, and I now realize that’s completely true. But back then I said, ‘Really? Really, he’s collaborative? Because he doesn’t come across as collaborative. He comes across as an asshole.’ ” Someone had to be: “Toy Story 2,” “Ratatouille,” “Cars 2,” and the forthcoming “Brave” were all going so badly, midway through, that their directors had to be replaced. Michael Arndt, who wrote the screenplay for “Toy Story 3,” observes, “Andrew’s primary allegiance is not to his fellow-filmmakers, or the characters in the story, but to the audience. When you look at things through that lens, there’s an imperative to be harsh.”

“Today’s service will be using the hashtag ‘#Jerrysdead.’ ” Facebook

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Stanton’s precepts are often invoked at the studio, particularly “Be wrong fast” or “Fail early.” He explains, “It’s like every movie is a kid, and no kid avoids puberty. Just dive through it—get that outline that should take three months done in one, so you get the inevitable bad stuff out of the way and have more time to plus the good stuff.” Another Stantonism is “Do the opposite”: if a woman is going to spurn a marriage proposal, Stanton will open up possibilities by wondering, “What if she said yes?” He urges writers proposing a fix for a balky scene to “finish the sentence”—to follow their change’s consequences to the end of the movie, to insure that it works throughout. His byword, though, is not tactical but emotional. Pete Docter, whose first directing job was “Monsters, Inc.,” says, “I thought the film was about clever ideas and bits, and Andrew kept saying, ‘What makes me care?’ ” A loyal dog or a syrupy score won’t do it. Lee Unkrich remarks that if Stanton “feels a filmmaker is telling him how to feel, you can see the red rising in his face—the red-thermometer face.”

Stantonisms are the closest thing Pixar has to a secret sauce. Michael Arndt, who came to the studio shortly before winning an Academy Award for his “Little Miss Sunshine” screenplay, says, “I thought they must have some foolproof system, some big Pixar story machine, but they actually just make it up each time as they go along. Pete Docter’s analogy is ‘Everyone holds hands and jumps out of the airplane with the promise that they’ll build a parachute before they hit the ground.’ ”

Yet there is also a purely mechanical aspect to audience arousal. Stanton’s home office displays the black field binoculars that inspired the face of Wall-E, the unlikely star of his 2008 film. He borrowed them from a friend at a Red Sox-A’s playoff game in 2003, then tuned out the game altogether: “I started bending them at the hinge and making them go happy and sad, and it began racing at me how I used to do that with my father’s binoculars. John’s Luxo lamp”—the architect’s lamp from Lasseter’s first Pixar short—“only goes up and down, but the binoculars’ fold would give me just enough feature and depth to hold your attention for a full-length film. The art directors later added an iris, which was a surrogate for eyebrows, and eyebrows are the feature, in people, that tells you that someone is thinking, that they’re alive.” (Fish don’t have eyebrows, either, yet on “Nemo” Stanton’s animators paid a lot of attention to “eyebrow mass.”) He considered his prize fondly: “I literally stole the flat brow of this pair, and the sad-sack bags under the eyes, the Buster Keaton quality that gave you a default sadness.”

The Braintrust was effusive when it saw the first reel. “It ended up haunting me for the rest of the film,” Stanton said, “because nothing else went easily. In fact, I don’t think I’ll ever make anything that will feel as divinely dropped in my lap as the opening of ‘Wall-E.’ ” The first reel has almost no dialogue. Lasseter says, “It was classic animation, where, as Chuck Jones”—the great Bugs Bunny director—“always said, ‘You should be able to turn the sound off and know what’s going on.’ But it also scared the crap out of Disney, and us, because our idea until then had been ‘Great animation has big stars saying witty dialogue.’ ” Stanton made audiences care about his workaday robot with exquisite storytelling and clockwork gags worthy of Keaton himself. In one scene, set in a derelict supermarket, Wall-E accidentally dislodges a bunch of shopping carts, which pursue him down a ramp as he flees in terror. When my five-year-old daughter watched it, she bent completely double, laughing as hard as I’ve seen anyone laugh.