Genesis Breyer P-Orridge's definition of a quiet week differs very much from most people's. After a couple of delays, we finally catch up on the phone, and apparently this is down time for the former Throbbing Gristle and Psychic TV singer. "I've been so busy all year that I actually have a couple of weeks doing very little," he explains. "Just chilling out, which for me will involve two DJ gigs, a talk, a poetry reading, etc. But for me that's quiet!" For most people, that would constitute a busy schedule, but if P-Orridge was in anyway put out by having to add an interview to the to-do list, it didn't show, and the supposedly prickly singer was friendly and outgoing throughout.

It's easy to imagine how the above would constitute an easy-going time for P-Orridge, given he's spent most of the last year working on his writing, performing with the latest incarnation of PTV and travelling the world promoting the wonderful documentary The Ballad Of Genesis And Lady Jaye, directed by Marie Losier, a surprisingly intimate glimpse into the world of this most controversial of icons. "I had to bail after four months of doing [the promotions] every week, because it was making me sick, actually sick. Every night, we were reliving losing Jaye and even the dog in the film died of cancer a year later, and I lost the house because we couldn't pay the mortgage without Jaye's income. So it was like, you lose the house again and again, you lose Jaye everyday and I just got really worn out, emotionally worn out."

The death of Genesis' wife, Lady Jaye Breyer P-Orridge, forms a central and tragic part of The Ballad Of Genesis And Lady Jaye, and, after going through such a trauma, it's only natural he would find revisiting it so difficult, especially given the nature of their uniquely symbiotic love. I refer to Pandrogyny, where the couple famously underwent extensive plastic surgery to resemble each other, becoming, in a way, one soul in two bodies (as well as a living work of art), and which was the initial focus of the movie. "2003 was the year Lady Jaye and I decided to get breast implants," he says, explaining how the film came about, "and make the Pandrogyny project a public project. Jaye said to me 'It would be really great if we had someone around who filmed everything, like Warhol at the Factory, and just documented all the process we're going to go through'. There was no idea of it becoming a film at all, it was documentation, mainly for ourselves. Within a week, we were playing a show at The Knitting Factory, and Marie was in the audience and was really touched by my poetry. She didn't know us at all, but she said she was a filmmaker and Jaye offered for her to come on tour with Psychic TV for two weeks. She filmed the entire tour and became a really special friend, and [from there] it just kept on going. She just started documenting our lives. At some point, just before Jaye dropped her body, it started to be a case of making it into a documentary, something we decided much more earnestly after Jaye dropped her body. Primarily in honour of Lady Jaye, to maintain her memory".

The Ballad of Genesis and Lady Jaye, beyond its welcome - for TG or PTV fans - footage of Genesis, acts as an elegy to Lady Jaye, who is probably less well-known than her other half, but who subtly becomes the focus of the film. This was clearly P-Orridge's intention. "When it comes out on DVD there's going to be a bonus disc with a lot more of Lady Jaye. There's a part in the film where she looks at the camera and says 'I've got everything I need to be happy because I've got Gen.' Well, we've got the whole 14-minute talk, the speech she was making about Pandrogyny, ethics and what we were doing, and why we were so in love. That unedited speech will be on the bonus DVD, as well as Sleazy [the late, great Peter 'Sleazy' Christopherson, who founded both Throbbing Gristle and Psychic TV with Genesis] talking about us too.

"Those bits weren't in the original film because we didn't have anything to do with the editing, we left it to Marie and didn't want to interfere. We wanted it to be what she saw, and the editing job she did - which she spent a whole year on - is amazing. But at some point in the editing process, she decided to not have any talking heads. She approached it as a collage, an 'elegy collage', as you said. And it worked - she made an amazing film! One of the things that's happened with the film is that the media has become much more friendly towards me. In some ways, it's humanised me where in the past the media has tended to demonise me. People see my mischievous side, as when I'm sitting on the keyboard, and they see how much Jaye and I loved each other."

Given Breyer P-Orridge's past interest in "extreme" art and music, perhaps such a personal project should come as little surprise, but it's still remarkable that he would allow such close access to what must have been a harrowing period after Lady Jaye passed away. "Like we said, the level of intimacy is gruelling, emotionally, for me. Jaye's way of explaining life and experience is that it's consciousness of who we are, and the body is just a cheap suitcase that we carry around. It's a philosophical way of dealing with the human body - she was always dissatisfied with the human body, and felt trapped in her body, in fact, [she felt this way] from being a child.

"It was difficult to allow someone that much access after Lady Jaye dropped her body. We don't remember the first year after the funeral, we don't remember doing anything, or seeing anyone. Luckily for me, our extended family took care of me. We were catatonic, basically, it was a trauma. The way it happened, out of the blue, with her breathing her last breath into me, was traumatic. It took maybe 18 months, and we were with Marie and we said 'Let's finish it'. It was really important to finish it, because it was Lady Jaye's idea. We had to finish it, as a matter of pride and respect of Lady Jaye's wishes."

Despite all the aforementioned sadness, The Ballad Of Genesis And Lady Jaye remains an uplifting experience, and you come out of it aware that you've experienced a celebration of love, something P-Orridge is keen to underline. "When we've been at screenings and Q&As, the most common reaction of people who've come up to speak to me is almost always, even if they're crying, 'I've always been afraid to really commit myself 100% to a relationship because I've been scared of being hurt. But now I've seen this film, I'm not afraid anymore. I realise how much love I've wasted that I could have had.' Isn't that a great thing to have happen from a movie? That people would not be afraid to be in love, and to be different?"

'Not afraid to be different'... I saw The Ballad Of Genesis And Lady Jaye at the London Lesbian and Gay Film Festival, and was initially surprised at the choice because, for all his idiosyncrasies, P-Orridge never struck me as being an LGBT figure, even with the Pandrogyny. In that respect, it was a real eye-opener, not just about him, but about the ways in which "alternative" sexual identities can be expressed, by anyone. It felt like a true work of "queer" art.

"We're not traditional LGBT people, are we?," says Breyer P-Orridge. "Derek Jarman, for me, is a queer filmmaker. 'Queer', to me, includes eccentric and being prepared to push through any stereotypes, even gay stereotypes. The people who have been the most puzzled by us have actually been the more 'traditional', neo-conservative gay people, who - and this is not in any way a criticism - really want to be accepted as normal and treated just like everyone else, as they absolutely should be. But sometimes they maybe become stereotypes of everything they were rejecting and, for us, we don't want to become just another stereotype. It's not about me becoming a woman, or Jaye becoming a man, it's about the divine hermaphrodite, and the potential of the human species to evolve in the most amazing ways, having no limit on what their body can be or what they imagine is a way of being. It's much more philosophical, magickal and evolutionary. We did an interview for ABC over here, because we'd been banned from Phoenix on account of me being transgender, and we knew they wanted 'bumper stickers', you know? So we said 'Transsexuals are the stormtroopers of the future!' [laughs]. In a way, we do believe that. Certain people in our species are waking up to the potential to have a different future to the one we've been offered."

In this context, the Pandrogyny is crucial, and in the way it bridges art and life, it seems unique. In the wake of Lady Jaye's passing, one could assume that Genesis would put the experience on hold, but that seems to be far from his mind. "It's our ultimate project," he says. "It's a process and a project. With everything that we decide to make public, that's when it becomes a project. On the very first day we met Lady Jaye, she took me to her apartment and dressed me in her clothes. She intuitively knew the trajectory of our relationship, and we kept on exploring that, privately, together - becoming two halves of the same whole. We wanted to blur together; if it had been medically possible, we would have had a vagina and a penis each. That would have been our maximum choice. Why should we submit to the programme [of DNA]? That's how we got back to the Burroughs/Gysin cut-up, and thought about cutting up DNA like literature or music. Can you edit biology and generate the third being? That's how we got to the revolutionary part: DNA has come to symbolise a deep sense of control; it's something most people just accept. It got more complex as the years went by, but we're still doing exhibitions and creating sculptures. We've been commissioned to do a book called Creating Sex and the Andy Warhol Museum in Pittsburgh have confirmed that they're going to do a retrospective of Breyer P-Orridge and Pandrogyny next summer."

In an era when so much art is being commodified, P-Orridge's commitment to the ultimate realisation of this unique project is refreshing.

Genesis makes it clear that recognition by the Andy Warhol Museum is a source of personal pride and gratification, and he is quick to reference his debt of influence to The Factory and Warhol stars like Candy Darling. As someone so notorious for his musical performances, notably with Throbbing Gristle, you get the feeling that it's been an uphill struggle for him to be recognised also as a major visual artist - he uses the word "vindication".

"Certainly in America, we're getting a lot more serious attention to our ideas," he says. "The word 'Pandrogyny', which we created - 'positive androgyny'- has started to filter into the language, as a new word with a lot less baggage. We can all define what this word might be, it's not meant to have a fixed definition. It's a form of freedom from the past. The art world started to accept COUM Transmissions towards the end, in '75-76, when we started doing museum shows, but the art world didn't want us to do music [as Throbbing Gristle]! They didn't think we were doing art, because we were doing music. We were always in the wrong camp, but we always wanted to do everything. We've never stopped making art, or writing essays [even during TG and PTV]. In the last two or three years, things have really changed. Lady Jaye and I started doing exhibitions together, and we were surprised that people loved our approach and were listening to what we were saying. The Tate recently bought our archives, so the art world has really started to take us seriously as the whole package. Life and art can be the same thing. Artists have been saying this for 100-odd years!"

After so many years of struggling against the establishment, touring, exploring every facet of art and life, you could forgive Breyer P-Orridge for being jaded, but far from it, and the supreme energy that inhabits him remains anchored in his relationship with Lady Jaye, something that comes up when I mention Yoko Ono's own struggles with the public and the establishment's perceptions: "The reason that we adopted Breyer P-Orridge was to say 'Jaye is equally as important. She's not doing this just because she's with me, she was already doing stuff before we met and a lot of the ideas are her ideas.' We're insistent: don't dismiss her because she's female! And don't dismiss this because her body's not here anymore. She's still vital to the project". It seems clear, then, that Pandrogyny may be one of the major artistic expressions of feminism in the last few years.

But, of course, it's impossible to interview Genesis P-Orridge without honing in on the music, and a chat about a DJ set where he spun Amon Duul II and Hawkwind records emphasises that, for all the 'industrial' reputation of TG, Genesis at heart is a bit of a psychedelic hippy. "Oh, absolutely. And it's been missed. The new line-up of Psychic TV that we have are the best musicians we've ever played with. We've done some singles: the first was Funkadelic's 'Maggot Brain' b/w 'Alien Brain', the second was 'Mother Sky' by Can, and the B-side was 'Alien Sky'. Next will be a Hawkwind cover! We take the structures of the songs and rework them [on the B-sides], so the 'Alien Brain' features vocal, and lasts 15 minutes. It was done in one take, with the whole band in the studio. We don't rehearse, we just go straight into the studio and lay it down. It's a fascinating project. We're trying to tell people not to dismiss this era just because there's been so much propaganda about hippies. Never be biased or prejudiced, and then you can make it your own. There are always more doors you can go through"

This ethos of constant exploration even extends to language, and throughout the interview Genesis substitutes "I" for "We".

"When we first met Burroughs back in 1971," he says, "we were hanging out in his apartment, somewhat in awe of him, we said to him, 'Do you still do cut-ups?'. He said, 'No, I don't really have to any more, because my brain has been rewired so it does them automatically!' That's kind of what's happened to me. Burroughs told me to always write every day, so that when you have a sudden revelation of meaning, in language, you're ready to document it and expand it. At this point, after 50 years of writing, it's become second nature to see words and break them down and reassemble them automatically. It's why I can improvise vocals on the spot. With 'we', it obviously means me and Jaye, but then, can we use 'we' when talking about before we met? In 1968, we started using 'E' for 'I'. Should we use that? Someone suggested we should just use 'they'!"

I'm uneasy to approach the subject of Throbbing Gristle, given everything that's been written about them, not to mention their various break-ups and Sleazy's tragic passing, but Genesis welcomes the chance to go over the band's legacy, especially when we start discussing the lyrics he wrote for the band, which he showcased marvelously at their last-ever concert in London.

"Most of the TG songs were originally improvised on stage," he reveals. "'Persuasion' was improvised on stage, 'Convincing People' was improvised on stage... On the other hand, 'Hamburger Lady', for example, was improvised in the studio. 'Discipline' was made up on the stage in Berlin, when Sleazy and Chris [Carter] came up with that amazing rhythm. We said to Sleazy, 'What shall we sing about tonight?' and he said, 'Discipline!'. And it became a classic! It varies... We're just doing the first Thee Majesty album in eleven years, and we go in with poems we've written at home. It's about looking at which words fit the span of the music and then seeing what happens. We're always looking not to simplify the words for the music, but to fit the words into the music."

Unlike some early industrial artists, Genesis is more than happy to talk about the genre TG helped name, never mind initiate, and he talks enthusiastically about more recent artists, such as Prurient, who are clearly indebted to Throbbing Gristle's legacy. "We didn't know [the industrial scene] was going to happen, we just knew that we wanted what we were doing to have a very clear separation from everything else," he explains. "The birth of something new, a new approach, something that was more contemporary and more modern. You can't plan those things, but then sometimes you can feel the zeitgeist. TG was four very exceptional people. You couldn't take any of those four out. Sometimes those things happen, and the right people are in the right place at the right time together."

As much as talking about writing inspires him, it's clear that TG's reputation for controversy is a wearisome subject. "It's been something that always frustrated me: people didn't even ask about the lyrics and take the songs in as being songs. They just focused on one or two that were more abrasive, and the shock value, and ignored the rest. It's one of the downsides of notoriety: the powers that be utilise anything like that as an excuse to dismiss what you do. But you just have to believe in what you do and, in my case, be patient."

Does he feel more satisfied now? "Actually, yes! PTV3 is far and away the most exciting group of musicians that we've ever worked with. They're all capable of playing technically but also of experimenting and improvising. Our live shows are never less than two hours and we have videos, light shows. Everyone's hyper-aware of each others' body language, and they can all tell the timbre of my voice. No matter how odd it is, the band is always there, totally with me." It's an osmosis that at times evokes Neil Young & Crazy Horse (a comparison that pleases Breyer P-Orridge no end), and listening to recent PTV3 releases certainly contains the mixture of beauty and chaos that defines The Horse at their best.

Through all the tumult of the last few years, from personal tragedies to his numerous artistic and musical heights, including recent performances, an album with Tony Conrad and a book of his life in pictures he'll be supplying texts for, Genesis Breyer P-Orridge remains a strong and unique person who constantly looks to follow his boundlessly creative impulses as far as he can. "We've always had a very long-term view of everything, and kept in mind the perspective of looking back at things from our death bed. Will we have achieved everything we hoped for by then or, at least, will it be as pure as we hoped it to be?"

The DVD and CD soundtrack of The Ballad Of Genesis And Lady Jaye are both out now