John Callahan, the quadriplegic cartoonist and subject of the new film Don’t Worry, He Won’t Get Far on Foot, fits right in among the free thinkers dotting the filmography of director Gus Van Sant. In a career spanning three decades, Van Sant has consistently gravitated towards those subversives and visionaries who go against the grain of mainstream society. That unorthodox streak can work to their benefit, as with the janitor genius of the populist hit Good Will Hunting. Sometimes, it’s to their detriment, as with the free-living drug addicts of Van Sant’s early arthouse sensation Drugstore Cowboy. Most frequently, though, it’s a combination of both. As seen in his biopic treatments for Kurt Cobain and Harvey Milk, Van Sant’s got a thing for martyrs, for those able to transmute the agony of their mere existence into great and meaningful works.

All of which has brought him back to Callahan, and to the famous Phoenix acting dynasty. Van Sant has tussled for years with the idea of a film about Callahan’s extraordinary life – a car crash left him without use of his legs or fine motor skills in his arms, but didn’t stop him from clasping a pen between his hands and illustrating his hilariously dark, darkly hilarious jokes. The project was initially conceived as a collaboration with Robin Williams, and rewritten several times as matters of scheduling or financing precluded a start to production. Williams’ death in 2014 could have permanently shuttered Don’t Worry, but Van Sant found a suitable replacement in a past collaborator.

“I started from scratch again,” Van Sant says during a curiously terse interview, possibly due to a shaky phone connection. “The other screenplays from 1997 and 2002 were written for Robin, and this time around, it was my first time writing for John Callahan, writing for the book. When Joaquin got involved, I started writing with the idea that he would play it. I still knew he’d have his own spin on it, though. So I wasn’t so much writing it for Joaquin as I was envisioning it with him in mind.”

A virtuosic actor who could not possibly care less about pursuing movie stardom, Joaquin Phoenix sounds a bit like one of Van Sant’s creations. The pair first linked up in 1995 for the black comical vérité-style crime yarn To Die For, in which a then 21-year-old Phoenix portrayed a student seduced into murder by psychotically ambitious newswoman Nicole Kidman. Since then, they’ve stayed close as their individual profiles have grown.

“[Joaquin] is intense, it’s true, but I’ve known him all these years and we’ve kept in touch,” Van Sant says. “We talk about a lot of things we’re working on independently, but this is our first movie together in over 20 years. He’s very hard-working. We went through the entire script, page by page. He wanted to make sure everything I was indicating in the story was something he was in sync with.”

They rehearsed for two weeks before the start of shooting, finding the character’s affect, calibrating his sincerity and sarcasm. As the film makes clear, Callahan was a complicated guy, a sensitive soul prone to jags of neediness or even cruelty. By his own admission, Van Sant didn’t know what to expect when he let Phoenix have at the character, though he had complete confidence in his leading man. The script includes some rather demanding material for a performer, in particular a rock bottom that finds Callahan dragging himself around the floor like a slug in an effort to retrieve a wine bottle that’s rolled under a chair. But when questioned as to whether these were difficult days on set, Van Sant sets the record straight.

“Working in the first hospital was hard, because of the rotating gurney,” he recalls. “It was old, sometimes it malfunctioned. But whatever scene we’re working on, we make it as hard as we can. If it’s not hard, we push it until it is. That’s what you end up doing, because if you sit there and you let it be super easy, you’re going to be phoning it in.”

Phoenix and Van Sant have achieved a creative synthesis that many artists spend their entire lives searching for, where intuitive understanding makes communication seamless if not unnecessary. That degree of closeness takes time to build, and in this particular instance, their bond is strengthened by their shared memory of Joaquin’s older brother River. Before River died from an overdose, he worked with Van Sant on My Own Private Idaho, perhaps Van Sant’s most widely acclaimed film. When I liken Don’t Worry to Milk in their reorganizing of one man’s conflicted struggle against adversity, Van Sant makes the counter-suggestion that the film is more similar to My Own Private Idaho or To Die For in its elliptical treatment of time. It does not seem coincidental that he names the two films fronted by Phoenix boys.

But if this conversation painted Van Sant as a man bound up in his own past, it also gave him ample opportunity to look to the future. He’s a man comfortable in seemingly any position or showbiz milieu, acting as executive producer to films in need of a push through production and cameoing as himself on Entourage. Most recently and outrageously, he appeared in the Jonah Hill-directed music video for Ain’t It Funny by Detroit rap maniac Danny Brown. The surreal, violent video casts Van Sant as the wholesome father figure on a sitcom with rot at its root, a bizarre gig by which he nonetheless sounds unfazed.

“To be playing a character, it’s good for a director. Reminds you of how difficult it is, to wear a costume and say lines. But I don’t know that I’ve got much street cred in the hip-hop community,” he deadpans.

His amenable attitude extends to his business dealings as well. Don’t Worry comes to theaters courtesy of Amazon’s fledgling movie studio, a somewhat disorienting logo to see pinned to a film by one of American independent cinema’s poster boys. But Van Sant is unintimidated by new horizons, stating that Amazon and other streaming platforms have “opened up tons of opportunities” for longform storytelling. When asked whether he’d ever try his hand at the limited series that his indie cohorts have been flocking to in droves as of late, he’s entirely amenable to the idea. He’s not at all concerned about the shift away from brick-and-mortar cinemas.

“Movie theaters really were just constructs of the past’s industrial cinema, where it was easier to get thousands of people to see one print at the same time,” he says. “Now, it’s a different industrial construct. You might see it on a smaller screen, but the original films were shown on nickelodeons, which had very small screens.”

With this, Van Sant places himself on the same frequency as Joaquin, or River, or John Callahan, or the defiantly different characters on which he trains his camera. He’s a reminder that indie is short for “independent”, pursuing his intimately personal thematic and stylistic whims wherever they may lead him. And that’s not always into critical favor; his last two films, the mortality meditation Sea of Trees and fracking drama Promised Land, have drawn mixed-to-poor notices from the press. In typically singular fashion, however, he has paid them no mind and in fact doubled down on his intrinsic Van Sant-ness to realize a long-gestating passion project.

In Don’t Worry, after Callahan places his first newspaper cartoon, he starts wheeling around town to excitedly show everyone who will give him the time of day. When a pair of art students pass him by without stopping to look, he hollers back at them with an unprintable word. And yet in that moment, Callahan seems only amused by their disinterest. One gets the sense there’s a bit of Van Sant in that moment: a man fully and happily committed to doing his own thing, everyone else be damned.

• Don’t Worry, He Won’t Get Far on Foot is now out in the US with a UK date yet to be announced