Is John Cameron Mitchell trying to go mainstream or doing what he always does with his new film about the loss of a child?

John Cameron Mitchell blasted into our consciousness in 2001 as the star/director/writer of a riotous adaptation of his own gender-bending stage musical, Hedwig and the Angry Inch. Five years later, he returned with the most sexually explicit American narrative film ever made outside the porn industry.

Shortbus was shocking, but more for the fact that it was one of the year's sweetest and most intelligent romcoms than for its scenes of unsimulated sex. The question was, what would Mitchell do next?

The answer, surprisingly, is Rabbit Hole: a mature and moving family drama starring Nicole Kidman and Aaron Eckhart, about a couple struggling with the death of their son, adapted by David Lindsay-Abaire from his own Pulitzer Prize-winning play.

An understated independent production with Hollywood credentials, Rabbit Hole looks like an attempt by Mitchell to come in from the fringes. Not so, he insists. "There's never really a conscious thing to do anything except what moves me. I have a cheap rent (in New York], so it's allowed me to choose what I want to do."

Reading Lindsay-Abaire's screenplay was a cathartic experience for the film-maker. "I lost a (younger] brother when I was a teenager," he says, "and the family was very wounded by it, and remains affected, and at the time you weren't really encouraged to talk about your feelings, so they kind of festered. People turned away from each other, to other things, to deal with it, and it wasn't always healthy. So this kind of brought up those feelings and made me understand my parents better."

The strain of losing a child causes many couples to break up; Rabbit Hole is about the ones who don't. Unlike the bereaved couple in Lars von Trier's Antichrist, says Mitchell, Becca (Kidman) and Howie (Eckhart) "find a way through the darkness and are heroically trying to get into the light". In this sense it is business as usual for the director; his previous two films also featured central characters who are "oddly isolated and imprisoned by their trauma, but they're valiantly trying to escape". He admires von Trier ("he's always testing himself formally and working with whatever demons are going on in him"), but would not have done Rabbit Hole if it didn't offer hope. "We're not trying to drag people in the mud and leave them there. I want a film to be something that adds to your life rather than subtracts."

Mitchell learned from the death of his sibling and, later, of a boyfriend who died through addiction, that "there's no standard way to grieve, (that] you can't skip stages, that you never know when they're going to come, that they come and go." When Kidman had her breakdown as Becca on set, he says, "I had my own little breakdown behind camera and we both felt great afterwards."

Kidman's character rejects religion and finds comfort in a scientific theory presented in a comic book. Mitchell identified with this. Although raised as a devout Catholic, he says that after his brother's death "the definition of God that I was taught didn't really make sense" and he too found solace in comic books and stories of science fiction and fantasy.

Given Shortbus, you might expect sex to figure in Becca and Howie's grieving process; Rabbit Hole is no Monster's Ball or Last Tango in Paris though. Becca constantly rejects her husband's attempts at physical intimacy, in a model of grief that Mitchell describes as brittle and waspy.

"She goes down a certain path where she puts the armour up and adds to it. You can see her as an odd, eccentric, lonely woman in a cottage off the coast of Maine, with lots of sweaters and cats." Thank God for sex, he laughs, "because it gets you out of the house."

Indeed, Shortbus was less about sex than about what sex is about. The characters are exorcising their demons through it and trying to connect. "It is about trying to get what's behind your skin closer to what's behind (someone else's] skin so there's meaning to life," offers Mitchell. "And that's what Rabbit Hole's about. And that's what Hedwig's about. They just use different metaphors. It's all about not being alone."

He traces his preoccupation with this theme back to his peripatetic childhood as the son of an American general and a Scottish schoolteacher. They'd move from base to base, and he'd constantly have to try and adapt to new surroundings and new people. On the one hand it makes you extroverted "because you have to survive," he says. "But there's also a strange alienation and you're always the new kid. You can be somewhere for 20 years and still feel like you don't really belong." For a long time being secretly gay, as he was then, heightened his sense of estrangement, while also adding another layer to his outsider view of the world: a key ingredient for being an artist.

"Your stories and your acting and your art become your family and your home. I'm used to temporary projects, which are microcosms of the way I grew up. I like that the films are over a couple of years and can find their beginning, middle and end. I don't think I'd be very good with one job over decades. I'd be itchy and restless."

The projects help him personally, too. Expressing the femininity that had been kicked out of him at school as Hedwig "made me a better person," he told me in Edinburgh in 2001, "because it eased me out and made me more comfortable with myself". Making Shortbus made sex seem much less scary to him. Rabbit Hole has "assuaged and calmed" the grief that ebbed and flowed in the wake of his losses, and helped him to understand his parents better.

"There's a time when you're angry at them and then there's a time where you see them as human beings. You're an adult yourself and you forgive, and hopefully they forgive you, and this is part of the process."

Kidman has been nominated for best actress Oscar for Rabbit Hole. Mitchell, meanwhile, is about to start writing a TV series, producing an animated feature, pondering the possibility of bringing Hedwig to Broadway, and adapting a short story by cult author Neil Gaiman.

"Neil and Amanda Palmer (his wife) have become close friends and he's offered me the use of his castle in Iona," he says excitedly. "We're working on adapting How to Talk to Girls at Parties, a Punk Rock-era tale in Britain that involves an alien girl on her semester abroad."

At the moment the setting is probably London, although he'd like to move it Glasgow. He attended a Benedictine boarding school in North Berwick from 1973 to 1975, when he'd watch Bowie and T-Rex (Glam touchstones for Hedwig) on Top of the Pops. "I would come back to visit my Scottish relatives through the Punk era. My cousin was into Gary Numan, and I remember when The Police were a bit punky. I would have liked to have seen the Rezillos in Glasgow," says Mitchell wistfully. "That would have been right up my alley."

• Rabbit Hole was released in cinemas yesterday