For a certain breed of music fan, it was like hearing that JD Salinger was returning from the grave to read The Catcher in the Rye at the Hay festival. On 25 January, Jeff Mangum, the reclusive former frontman of Athens, Georgia cult legends Neutral Milk Hotel, announced his first major live appearances since he silently retired from music more than a decade ago. To the thousands of fanatics of Elephant 6 – the US musical collective dedicated to all things buzz-fi, psychedelic and anti-slick, of which Mangum was a key member – this was astounding news. And then he topped it: he'd be coming to the UK for the first time since the final Neutral Milk Hotel show in 1998, to curate the All Tomorrow's Parties festival in December.

For many years, the prospect of Mangum making any sort of serious return had been as unlikely as the Smiths reconvening. Neutral Milk Hotel released only two albums in their lifetime – 1996's berserker-folk sprawl On Avery Island and 1998's follow-up In the Aeroplane Over the Sea. That second album was little more than a curiosity on release; a scuzzy, unhinged album inspired by the story of Anne Frank and Mangum's recurring dreams of a Jewish family caught up in the Holocaust, given a magical, surrealist sheen by its archaic penny-arcade artwork and lyrics about two-headed foetuses in formaldehyde jars, burning pianos and semen-stained mountaintops. Those who heard it adored it, enough that the pressure of their passion contributed to Mangum disappearing from view. But few did hear it, at least at first: that final Neutral Milk Hotel show, at the Underworld in London, was barely half-full. That changed over the following years, as the album slowly became recognised as an alternative milestone – feted by Arcade Fire, Franz Ferdinand and even Simon Schama, filtering ever-higher into best-ever lists across the alternative media and growing in sales to the point where it still shifts around 25,000 every year. Mangum, though, was hardly to be seen.

Never the most well-adjusted character (many of his songs were written during all-night sessions brought on by night terrors, and sung to the ghost in his haunted wardrobe), he was acutely uncomfortable with his new status as a cult hero. "Jeff's a very private person," says fellow Elephant 6 mainstay Bill Doss, co-founder of one of E6's other key bands, the Olivia Tremor Control, "and kids were freaking out over him. [They'd] be following him around, these little packs of kids staring at him. It weirded him out in a way, and he just sorta backed off."

In the decade between the beginning of NMH's indefinite hiatus and this year's announcement, word of Mangum's activities seeped out like a faint voice amid radio static. He'd turned down an REM support slot for their Athens hometown shows. He released an album of field recordings from the twice-a-decade Bulgarian folk festival Koprivshtitsa. He hosted a graveyard slot radio show on New Jersey's non-commercial WFMU station, calling himself Jefferson, immediately quitting once unmasked. He played a one-off show in a pub in Auckland, New Zealand, with his friend Chris Knox of the Kiwi band Tall Dwarfs.

Those were the unremarkable events. His ex-girlfriend Laura Carter claimed he'd had a breakdown and would spend days on end staring at his apartment wall in paranoid panic, or shuffling back and forth to a local Dunkin' Donuts in a pair of threadbare slippers he never took off. He'd become obsessed with Y2K scaremongering and started stockpiling rice.

The rumours mounted up: he was travelling the US from Nova Scotia to Arizona like a folk-rock Forrest Gump; he was planning a hot air balloon trip across the Atlantic; he was holed up in a monastery; he was starting a new career as a sculptor. Only one thing was certain – he wasn't making any new music.

A rare interview with Pitchfork in 2002 shed a glint of light upon Mangum's frame of mind at the time: "I went through a period, after Aeroplane, when a lot of the basic assumptions I held about reality started crumbling. I guess I had this idea that if we all created our dream we could live happily ever after. So when so many of our dreams had come true and yet I still saw that so many of my friends were in a lot of pain … I realised I can't just sing my way out of all this suffering."

Then he began popping up again. In 2008 Mangum appeared at several dates of the Elephant 6 Holiday Surprise Tour to perform one song, Engine, the first NMH material he had performed live in seven years. When Chris Knox suffered a stroke, Mangum played a five-song set at a benefit gig, and last December he performed 10 songs at a Brooklyn loft party. The red mist is clearing, and Mangum's re-emergence couldn't be more timely.

For 2011 is bringing a wave of bands who have adopted Elephant 6's aesthetic of outsider music, made in a spirit of derangement. The Rural Alberta Advantage, based in Toronto, share NMH's uplifting sense of no-fi abandonment in the face of personal anguish, as evinced on their excellent second album, Departing. "I remember when I first heard [In the Aeroplane…]," singer Nils Edenloff says, "and it struck me as really beautiful, like the melodies themselves were perfect. And the emotion to it, you felt like he was singing directly to you. In a way we're trying to take those sort of elements and do our own thing with them and hopefully bring them to a less frightened audience – taking powerful, emotional songs and making them celebratory."

Over in New York, meanwhile, the Morning Benders are exploring the lusher end of the E6 oeuvre. "Elephant 6 was the gateway for me," frontman Chris Chu says. "They seemed to be bridging that tradition from the 60s to a more modern, more indie approach. It was exactly what I was looking for, a new take on that stuff. It sounded cool, like these guys were bashing around in the garage."

And while acts as far-flung as Australia's Tame Impala and Starfucker are plundering E6's vaults for influence, New York's the Terror Pigeon Dance Revolt! perhaps do it best. They released a self-titled debut album in 2010 that was an amalgam of all the central E6 bands – NMH's celebration of the uncelebratable, the acid-fried pop of the Olivia Tremor Control and the bubblegum psychedelia of E6's other founding band, the Apples in Stereo – but with a dancefloor edge. "I'm trying to marry the feeling that a lot of Elephant 6 recordings have of a bunch of friends in a room making music, plus super-sleekness, super-poppy jams," singer Neil Fridd says. "I don't think they're unmarriagable, but they are difficult to put together."

TTPDR! also follow the Elephant 6 tenet of "chaos gigs": they hold pillow fights and wrestling matches at their shows, and Fridd often plays dressed in a suit made entirely of stuffed toys. It's an ethos inspired by E6 act the Music Tapes. "In New York they got us to write down all of our dreams and make a wish," Fridd recalls with no little sense of wonder. "We ended up out on the street burning the dreams on a little fire and everyone would burn it and then run and jump over it. So a crowd of 200 people, one by one, went through and jumped over this fire."

Such eccentricities were commonplace at early E6 performances where, according to Robert Schneider, the Apples in Stereo's frontman, "the idea of getting through a song casually and playing it all nicely was offensive … 50% of the songs didn't make it all the way to the end. Our shows felt like a really fun train ride, but falling off the track and rolling sideways down the hill, but somehow it gets to the bottom and it's maybe sliding on ice but it still keeps going."

Elephant 6 was founded in 1992 by four friends who grew up together in Ruston, Louisiana, obsessed with the Beach Boys, Black Sabbath and 60s psychedelia. Those four were Schneider, Mangum, Doss and Olivia Tremor Control's Will Hart. Although all were southerners, E6 began in Denver, Colorado, where Schneider formed the Apples in Stereo, though both the Olivia Tremor Control and Neutral Milk Hotel based themselves in Athens, Georgia. E6 adhered to a manifesto of familial collaboration (on early tours the Apples in Stereo and Neutral Milk Hotel were essentially the same band, fronted by Schneider or Mangum for their individual sets) and the celebration of home-produced music.

"We'd developed a tolerance and a love for really lo-fidelity recordings and sloppy musicianship," Schneider says. "We had a hatred of slick musicianship and recording. I hated indie, I hated all modern music. To my ears it had the most offensive sound quality, the shimmery, late-80s, early-90s sound made my skin crawl. There was a repulsion for the sterile feeling on all major label and studio-recorded releases at the time. I had a mission to take down popular culture. My vision starting Elephant 6 was this perfect pop world, completely pure and completely untainted by slickness or money or commercial interests."

Having built a cult following thanks to impressive releases by bands including Beulah, Of Montreal and the Minders, as well as the three core bands, E6 floundered towards the end of the 90s. The ever-expanding E6 family had become unwieldy and, post-Aeroplane, Mangum wasn't the only member with personal problems. Schneider went through a painful divorce, which led him to give up running the E6 record label and quit the collective, while Will Hart, who had multiple sclerosis, was unknowingly developing legions on his brain which made his behaviour erratic, ultimately splitting OTC and contributing to the collapse of E6's central social group.

"None of us knew why, we just knew he was acting crazy," Doss remembers. "His brain was fritzing out and he was having a difficult time trying to figure out why. It was like getting divorced: all of a sudden I hated him, for no reason other than I was confused. We didn't speak for years."

For six years Elephant 6 lay dormant. But just as Mangum has reanimated, E6 activity has resumed. In 2005, Schneider travelled the US collecting contributions from Mangum, Doss and Hart for the Apples in Stereo's synth-pop classic New Magnetic Wonder, the first album to use the E6 logo since the collective's disintegration. Then, in 2008, the Music Tapes staged the Elephant 6 Holiday Surprise Tour, featuring Mangum, Doss and Hart. "In terms of giving you a fingerprint of what Elephant 6 was like and the feeling and the chaoticness and problems, it was awesome," Schneider recalls. "It was this totally amazing, shapeless musical circus. It was what Elephant 6 was."

In addition, the Olivia Tremor Control are recording together again, and hope to release an album this year, just in time to surf the second wave of E6.

But why is the collective's influence emerging now? "There's been a huge surge of people making music," Neil Fridd says, "and if you're making music at home on your computer it's going to sound lo-fi. It's like hearing a bunch of friends try to make music in a bedroom."

"There's been a 60s garage and pop revival," Chu suggests, "and also home recording is becoming more popular and lo-fi recording is becoming more fashionable. That combination has intuitively led people back to Elephant 6."

But it's E6's community spirit that most inspires the Rural Alberta Advantage. "The idea of a group of people working together," Edenloff says, "trying to help out all their friends and creating something special among themselves and then having it get a wider audience – everyone wants that. Elephant 6 did it really well on a larger stage."

This September, E6 reaches its largest stages ever. Cherish it, before it disappears again on that aeroplane over the sea.

All Tomorrow's Parties Curated By Jeff Mangum takes place from 2-5 December at Butlins, Minehead. The Olivia Tremor Control and the Apples in Stereo will also be appearing.

The psychedelic south: Deerhunter's Atlanta

'I'd rather not be doing this interview," Bradford Cox says, wincing. "But you had the audacity to invite yourself into my world. And if someone flies to Atlanta to talk to me, I better treat him with respect."

Given the American south's reputation for hospitality, it's fascinating that Cox's definition of "respect" includes threatening to "rip you a new asshole if you paraphrase my emotional moment of transparency" when my tape recorder runs out at an inopportune moment. Likewise his threat – said with a smirk, admittedly – not to let me leave his house until we've redone the interview to his satisfaction. This comes after 13 hours in his company. Luckily, no amount of cat-and-mouse tactics stops him from being compelling company. It's like scrapping with an over-achieving, extremely lucid teenager.

As Deerhunter's lead singer, main songwriter and co-guitarist, Cox is proof Janelle Monáe isn't Atlanta's only shining star. Though Deerhunter formed in 2000, the band only settled on their current lineup when Cox's schoolmate Lockett Pundt joined on guitar in 2005. The brilliant Microcastle album (2008) raised expectations, made good by last year's Halcyon Digest, which expands the band's uniquely eerie, heavy-lidded and cryptic vision. "A southern gothic take on glam Berlin. Exile on Main Street meets Low meets Tusk," Cox reckons, though that leaves out the doo-wop influences that set Deerhunter further apart from the uplifting crescendos of North America's most successful alternative bands, from Arcade Fire to Grizzly Bear. On top of this, Cox's beguiling and troubled lyrics (the recent single Helicopter is based on the story of a Russian rent boy reputedly thrown to his death after losing his youthful allure) also demand exploration.

Unfortunately, 30-year-old Cox is done with exploring himself. He admits that in his teens he would interview himself in the mirror, fantasising about the attention. Not any more. This is partly due to having inherited the genetic disorder Marfan's syndrome. People with Marfan's tend to be unusually tall and skinny, often with weakened lungs and spine. "People think I'm a junkie because of how I look," he says. But as a former inveterate blogger at frequent loggerheads with fellow bigmouths, engaging with the rest of the world has left him weary and wary. "I think I confuse more than anything when I talk," he says. After giving no UK interview for two years, Cox accepts my suggestion to try something different – to show me around his Atlanta.

He picks me up in his Volvo, and after driving around the city's industrial outskirts, he points out Lenny's, "a dive bar where Cole [Alexander, of the Black Lips] would do weird improv stuff, really chaotic and energetic". Cox is still at it today, creating music almost to the exclusion of socialising. "I don't like going out," he says. "Except to one of three restaurants. I'm very rigid like that." He made an exception for a New Year's Eve party, to his chagrin. "These young fucking art school kids attacked me because I took off Duran Duran and put on [experimental minimalist] Tony Conrad. I don't understand what kids want any more, and I'm not interested in catering to it. All they want to do is dance and fuck, and those are two things I'm completely incapable of."

Cox has identified himself before as gay, but now claims he's asexual, "because I'm a virgin". While his teenage pals were having fun "on stained couches, I was in hospital, addicted to painkillers after spine surgery, addicted to that blissed-out feeling that I think has a lot to do with my taste for ambient music".

Drinking sweet black tea – "the table wine of the south" – in Sauced, one of his three food stops, Cox talks about the music he listened to as a kid. He was just 10 when he heard the Velvet Underground, from which he moved on through 60s garage, 70s krautrock and 80s post-punk. "But we've always tried to blur things further," he says. "Like the sound and the fury of a show more than the actual notes." He pauses. "We've always been dismissed by avant-garde people as too pop, and by pop people as being fucking freaks."

Over a late brunch the next day, he adopts his usual posture of perching, legs drawn under him like a gigantic bird. Relaxed conversation is clearly off the menu. Daylight makes him nervous, he says, "useless" even, and he fills time by eating, running errands and visiting family. But at night, there's no stopping him. He recently gave away four albums – 49 songs in all – online under the title Bedroom Databank. "You come off on tour and there's this crippling depression, like, what do I do with myself? I improvise. Fuck record labels and commercial criticism – let people hear what it sounds like when I'm making music without knowing there's an audience, like I used to."

We drive to neighbouring Marietta, to visit Deerhunter's rehearsal space, Notown, a suburban carriage house full of band stuff. Cox sits behind the drumkit and starts playing the krautrock motorik pulse, before slumping on the sofa. "I get irritated when I see all this equipment and think we should be doing more. But everybody else has girlfriends and they're lazy. But I'd probably want to settle down too with some nice girl, or guy, or whatever I fancied at the time. People with kids, I'm often struck by jealousy. Because my parents love me unconditionally. They were supportive even when we fought, so I'm not terrified of failure like many people I know."

He suddenly springs up. "I'll take you through the process. I set up a shitty mic and fuck around with a guitar until something melodic happens. I usually come up with a vocal feeling, trying to sound open and vulnerable and androgynous. That's inspired by John Lennon, how he always sounded like a little boy. Then I just rap stupid shit. And then I move on to the next one." He plays me his last effort, a slice of happy/sad pop called Right of Way that, given its origins, is breathtakingly good. "Thanks. What you're hearing is the sound of someone really depressed because they can't write. It's a shit B-side at best."

He then suddenly decides I should meet his parents. "You gotta interview them!" he barks. "I get my strength from my dad and my punk from my mum." Cox's love of 50s rhythms also comes from Jim Cox, a Fats Domino, Little Richard and Coasters fan. "Dad was a badass," Bradford grins. Dad says of son: "He was creative from the time he was cantilevering building blocks. You couldn't mould him."

"I was an emboldened, precocious kid," Cox says as we drive to his mother's house. "In middle school, my best friend and I would hold hands just to attract this wild energy. I always had a thing about teenage mental institutions. I read that Lou Reed's Metal Machine Music was very therapeutic for shock therapy. I relate to those who find solace in dissonance and chaos."

His mother, Edith, who also has Marfan's, recalls Bradford's childhood "was ruined" by illness and bullying. But art and music saved the day. "When he was 12, Kurt Cobain was his idol, and Brad suddenly started playing guitar. Before that, he'd write and draw stuff that was just not usual for someone his age. I have boxes of it upstairs."

A box labelled "Keep Forever, Ages 8-11" is retrieved. "Even in my youth, I was a cynical dick," Bradford says, searching through the cuttings: "Flame and aerosol can/ Have you lost your path in red eye watering embers?" was written when he was eight.

"Aren't you glad I kept these?" Edith beams.

The daylight gone, Cox has brightened up, and suggests we eat tacos. "And then I'll take you to my house."

In a messy, dim and paraphernalia-strewn bedroom ("My sanctuary"), fit more for a student than an adult, he says: "Ask me the questions again, and you'll get better answers. Starting now." I ask why he is a misanthrope. "Why are you a journalist? That's the summary of this article. Do you really think I am?" You act like it, I say. "I don't disagree with that. But misanthropic people don't cry at films like I do. You just see me in the context of being interviewed. For crying out loud, you have me under a microscope."

As if suddenly remembering his dad had raised him "to have a strong stomach, and not be self-pitying", Cox softens again. "Nothing replaces seeing someone appreciate my music, their eyes closed, singing along, and telling me after the show how much it means to them. You can't be some cynical, whiny-arsed artist, shouting: 'I want my space!' There's nothing but gratitude."

We call it a night and he drives me home. "Thanks, it's been fun hanging out," he says, and he's gone.

Deerhunter tour the UK and Ireland from 25-31 March