'A young boy puts a feather into his mouth ... " So, in 1993, began Jeff Noon's first novel, Vurt. It was something the like of which had never been seen before, and it established Noon – then a struggling 35-year-old playwright earning rent by working in the Deansgate branch of Waterstones and writing at night – as a figure of major promise in British science fiction.

Twenty years on, Vurt is being republished in an anniversary edition with three new stories, but the Noon who wrote it is, if not a forgotten figure, then one who never quite achieved the recognition that seemed his inevitable due. The path has not been smooth. He had difficulties with drink and panic attacks. His work ploughed off in an experimental direction that made him a hard sell to mainstream SF fans. He left the Manchester that his early fiction so powerfully claimed as its own. And then, for about 10 years, he more or less vanished from sight. As he says: "If you step out of the public eye, which I did – I stopped writing novels – then people will forget about you."

When I ask Noon whether he might have had a conscious desire to duck fame, he emits a wheezy laugh. "Oh gosh! What a time to take time off when you're nearly very famous! You couldn't have planned it in a worse way, could you?"

His fans have always been there, though. It's often said of the Velvet Underground's first album that very few people bought it when it came out, but that everyone who did started a band. Noon's books are in that sort of category. When Steven Hall came to write The Raw Shark Texts, it was as a direct nod to Noon that he located the portal to an alternative universe in Waterstones Deansgate.

"In science fiction, once a generation there are one or two voices that capture the times the same as bands do," says the comics writer and novelist Warren Ellis. "In the 50s, it was Alfred Bester who wrote like cool jazz and Madison Avenue. In the 60s, Michael Moorcock happened at the same time as psychedelia. In the 70s, Joe Haldeman and Joanna Russ sounded like late-period acid-rock. In the 80s, it was William Gibson and the cyberpunk crew. In 1993, post-rave, where things were still jumping but they were starting to get a bit dark … Jeff Noon was the sound of post-rave."

It's hard to recapture the sense of how strange and beguiling Vurt was when it came out. It was set in a phantasmagorical alternative Manchester in which humans mingled and mated with sentient dogs, robots, telepathic "shadows" and creatures from – or contaminated with – the titular "vurt", a parallel world that was some unspecified mix of consensual hallucination, virtual reality game and drug trip to which you gained entry by sucking on coloured feathers. The thing about the vurt world, though, was that it was in some sense real. For everything from our world that got lost in the vurt, something from the vurt world came back. The novel's protagonist, Scribble, had lost his sister Desdemona to the vurt and got a dribbling, many-tentacled Thing from Outer Space in return. Vurt follows his attempts to find her.

Vurt and the books that followed – there was a sequel, Pollen, and a prequel, Nymphomation – elaborated a fluid mythos that combined rave culture, druggy fantasy, intimations of cyberspace, weird maths and overlays of Alice's Adventures in Wonderland (an abiding obsession registered in all Noon's books) with classical myth and English folktale.

Its pervasive sense – and it's a sense that runs through all of Noon's writing – was of borders melting and fusing, and of everything getting distinctly horny. Pollination, incest, cross-breeding, viral spread and chthonic mythology are governing metaphors, extending, finally, to the idea of language and even digital information as systems of polymorphic generation. The critic Michael Bracewell has talked of Noon's "sexually reproductive texts".

It was a bizarre world – Noon says he is more interested in "subject matter and atmosphere than character and plot" – yet an exuberantly propulsive story ran through it. "There are two drives I have," he says. "One is towards experimentation. The other is towards campfire storytelling."

Though he seemed to come out of rave culture, Noon was never himself, as people assumed, part of the Madchester scene. "I was very much an outsider," he says. "I was interested in it but I was never part of it and I never took ecstasy – I've never been that into drugs, apart from alcohol … probably because I know I'm an addictive personality so I'm always trying to control it."

Noon gave up drinking around 15 years ago, because "I had to" he says. "If you want to know the hideous details, I used to book into hotels – really cheap hotels in Manchester – for a couple of nights. Just buy wine, and orange juice, and aspirin.

"I used to cover the mirrors up with the hotel towels. I couldn't stand the sight of myself. I've always had problems with mirrors – ever since – even though I haven't drunk in such a long time. In Falling Out of Cars – his last novel before his years of silence, and his farewell to Manchester – all the mirrors are covered up in that book … covered up or broken. That definitely comes from that period."

It ended, says Noon, when "about three-quarters of the way through writing Nymphomation, I suddenly realised this was ridiculous. It was – not killing me, but … it was making me ill. I'd get friends making comments about it, which I couldn't stand ... I thought: 'I have to stop this.' And the only way I could do it was to stop writing. I wasn't a social drinker, at all. I could go out to the pub with my mates and drink a few pints – nothing. I was using it purely to fuel writing … So I thought: 'I have to stop writing.'"

Giving up drinking, Noon tried writing sober, and found he was able to: the connection was severed, but it didn't make his work any less peculiar. In Steven Hall's view, "at the end of the 90s, he sort of took over BS Johnson's role as our one-man avant-garde."

His avant-gardism was never exclusively literary. Music and the visual arts are central to the way he approaches his literary craft. It was while touring nightclubs ("a ridiculous concept now of course, but at the time it was something that people did") with authors from the rave-lit anthology Disco Biscuits, for instance, that he hit on his future direction. Listening to a reader before him, while he waited to go on stage, he became aware that techno music from the next room was "pumping away – doosh doosh doosh doosh, four-to-the-floor – and it was interfering with the reading in quite an interesting way. It suddenly came to my head and I turned to Sarah Champion [the anthology's editor] and I said: 'I wonder if you could do a dub version of a story.' I couldn't get that idea out of my head.

"By dub, I mean specifically referring back to early 70s reggae, when people like Lee "Scratch" Perry and King Tubby would manipulate an already existing tune on the B-side of a record using silence, empty space, pulling the faders down to reveal the skeleton of a tune ... " Noon started to "remix" sections of his own work. The first time he actually saw music software, he says, "I was astonished. I was jealous. He could take a piece of music and turn it upside down, stretch it, slow it down, remix it ... everything, with all these amazing buttons. And I thought: 'why can't I do that?' I was looking at different aspects of electronic culture and how that can affect prose. So what you call experimentation was to me a natural process of following that and trying to manipulate language in the same way that a musician manipulates music."

This new style was on show in his 1999 novel, Needle in the Groove, and in 2001's small-press rarity, Cobralingus, Noon developed his remixing techniques into what he called the "Cobralingus engine" – applying a series of processes to text, and incorporating "samples" that ranged from Shakespeare or Robert Herrick to lists of racehorse names. In some ways, his approach recalls the cut-up techniques developed by Brion Gysin and William Burroughs, though, says Noon, "I hadn't actually read any Burroughs at the time, and I still have some difficulties with him. Burroughs was always great at destroying language and I wanted to remix it so that out of that soup of words – again to go back to that organic process – something new would emerge."

Noon sometimes speaks as if writing novels – a form he feels is still too grounded in the 19th century – is fourth or fifth on the list of things he is interested in. He has been an art student, a punk musician, a playwright, and during the years he wasn't writing novels, he was trying to break into screenwriting – "Ten years of ... oh God, you don't want to know ... " – and he still says, "I love film more than I love novels."

That "dark era" of not publishing ended quite abruptly in "a moment, on a train, where I sort of thought, right: no more of this". Noon went back to a draft manuscript he'd written two years previously, called Channel SK1N: the story of a Simon Cowellesque entertainment mogul and a young pop star who starts to receive television signals on her skin.

Noon made a conscious decision to self-publish it as an ebook, attracted (after years of ideas "backing up") by the immediacy: "You'd finish something and you'd put it out." His post-gap publishing career is a typically fecund and peculiar one. Using his website, metamorphiction.com, as a sort of hub, he's publishing electronic versions of his back catalogue, running a number of collaborative projects with musicians and other writers, and using Twitter to put out dozens of 140-character fictions he calls "microspores" ("Escher had an idea for a story. It began, 'Escher had an idea for a story. It began, "Escher had an idea for a story. It began, "'Escher …").

The lists of numbered ideas – now in the thousands – that he has poured into Moleskine notebooks since the 80s are now pouring online: "The spores have become my ideas journal." A collection of remixed spores, Pixel Dust, is in the pipeline. He talks excitedly about online poetry subcultures, hypnagogic pop, liquid culture and digital ghosts. A vast project called "Electronic Nocturne" considers what post-digital culture might look like. "We're so entrenched in the digital age that we don't think it will end – but, of course, one day it will. I've been trying to imagine what will come after that and it's quite a difficult thing … "

His latest offline infatuation is comics, which he sees as the ultimate example of the borderline works he likes to call "avant-pulp". "There's no high and low art for me. That's why I go on about the avant-pulp. What I tend to do, really, is miss the middle out. The middlebrow novel has never really interested me; these Booker prize novels full of feeling and observation and all this stuff about human life or reality, whatever that is. That's never been my thing.

"I've always gone for either the avant-garde or really populist stuff – and I've always tried to fuse those two. I try to explain it as being as if James Joyce had written The Big Sleep. How brilliant that would be!"