In the heart of Pearl Jam's Seattle HQ, their singer Eddie Vedder contemplates what it felt like to be one of the two people who were, to the wider public, the faces of grunge. The other was Kurt Cobain, whose band Nirvana have been written into the rock canon, selling 10m copies in the US of their second album, Nevermind, released in September 1991. A month or so earlier, Pearl Jam had released their debut, Ten. It's sold 13m in the United States so far. Such success would exact its price from both men.

When Pearl Jam became successful, Vedder's first response was to open himself up. He'd write back when fans sent letters about his lyrics, questioning him about depression and alienation. But the letters turned into an avalanche. Then fans started coming to his house. A girl who believed Vedder was Jesus and had fathered her two sons by raping her almost killed herself by ramming her car into the wall of his house.

"One of the reasons you're protecting yourself is because you've been forthcoming with your emotions," he says. "So you have to build a wall. And now people are driving into the wall. That's what fucks with your head. I felt like my brain was a whore and I was getting mindfucked."

Like Cobain, Vedder was being torn into two directions. He was grateful for Pearl Jam's success, for the way it had changed his life. But he didn't want all his life to change. Vedder was not one of the "industry kids who they groom on the fucking Disney channel and who do what they are told". He wasn't prepared to be America's in-demand rock star – it was like "being strapped to a rocket ship. But some of us weren't built for speed." He hated that he had lost control of his own identity, his face cropping up on billboards and magazines, crowding him. At the 1992 Roskilde festival in Denmark, he found himself attacking bouncers (who were attacking a fan); he'd forgotten he wasn't in the crowd any more. Cobain, similarly alienated, retreated into heroin and killed himself. Vedder retreated into himself. He says Gus van Sant's 2005 film Last Days – a fictionalised account of Cobain's end – nails "that weird malaise, that feeling of almost looking at your life from outside. 'Is this us? Is this me?'

"I was almost overwhelmed by it all," he says. "I had this house – not a giant house, but three or four nice rooms, and a jukebox. And it had this laundry room, and I would sit in there with an ashtray that I trusted. It was like the world couldn't get me in the laundry room."

More than a decade and a half later – and more than 20 years since "grunge" was coined to describe the metal-punk hybrid of the Pacific northwest – Vedder is in Pearl Jam's vast HQ, home to everything from their rehearsal space to fan club to guitarist Stone Gossard's rescue dog. Here, hidden away on an industrial estate, they clock in and out of their shifts, a return to normality which has enabled them to survive.

"Every third person was shooting heroin," says Gossard, remembering Seattle when Pearl Jam first started. "It was the thing to do." But Pearl Jam's drug use was "done early". Guitarist Mike McCready says they were more likely to be killed by drink driving. "Or you'd hook up with a group of people you've never met before at a club. Then all of a sudden, you're with a bunch of guys that want to stab you."

But most of the career pitfalls were faced by Vedder, whose fondness for "tomb-stoning" off cliffs into the sea led the Red Hot Chili Peppers to call him "Crazy Eddie." Later, he took that death-or-glory approach into his band. "We'd be playing gigs and he'd climb up girders," says McCready. "He'd be gone a long time. And we'd be like, 'If he falls, he's gonna die.'"

Vedder is complex. He is often perceived as a rock version of the worthy do-gooder – not a Bono, but certainly at the earnest end of things. But bassist Jeff Ament insists he's "fucking hysterical". And he has a prickly quality to him, although it's hard to know how much is interview performance. Within seconds of our meeting, he explains that he relaxes by throwing axes, then produces a photo of his daughter in front of the target. She doesn't stand there when he throws, he reassures. "I've never been a calm, midrange type person," he says.

So what enabled him to survive when Cobain didn't? Vedder thinks his "inbuilt survival instinct" might have been the difference."We had different things driving us, but we were parallel trains," he says. "You look at it objectively and you think, 'What could be so fucking hard about being in a band?' But if you're coming from a place that's real, it's much harder."

Although Nirvana took grunge mainstream, Pearl Jam's Gossard and Ament had been among its pioneers. They were founder members of arguably the first grunge band, Green River, which came together in 1984. When Green River broke up, the pair furthered an unfashionable interest in classic rock with their new band, Mother Love Bone, honing the rock-meets-punk formula that propelled Pearl Jam. When MLB singer Andrew Woods died after a heroin overdose in March 1990, a few weeks before their debut album was scheduled for release, that band's career was ended. Gossard was devastated, and started writing material that fitted his mood. After a few months, he called his old schoolmate McCready – a struggling local guitarist who had given up on music – to come and play. Ament joined them, and a new group was born: Mookie Blaylock, named after a basketball player. Mookie Blaylock signed to Epic, but worries that they might be infringing the sportsman's copyright led to a name change to Pearl Jam.

"I was on acid," remembers McCready of the day he heard about Woods's demise. "It was a fucking weird day! If that hadn't have happened I wouldn't be sitting here." In fact, the early days of the band owed everything to chance. One was sending a tape to ex-Chili Peppers drummer Jack Irons in the hope he might join them. Instead Irons passed the tape to Vedder, a basketball buddy who sometimes sung in a San Diego band. Vedder mailed the tape back to Seattle, lyrics added which told stories about a man who discovers his father isn't his real father and embarks on an Oedipal murderous rampage.

The band thought they were funny. They didn't realise they were partly true. When he was 12, Vedder found out the man he thought of as his dad was actually his stepfather. His real father was someone who Vedder had known as a family friend, but who had died of multiple sclerosis. Still, Vedder says, he feels a sense of "adolescent disturbance", but compares his lyrics to the writing of Virginia Woolf or Edward Albee, saying that laughing at things that are "absolutely brutal" is part of coping. He turned his anger into, he says, into "positive energy" – the opposite of Nirvana's nihilism.

Pearl Jam's other members have their own theories as to why their band survived. Luck is mentioned often. Drummer Matt Cameron (who played on the first Pearl Jam demo, but only became a band member in 1998) says he was amazed to find, after joining from Soundgarden, that the band held meetings – talking problems through was anathema to his former band, who were "eaten up by the business".

But all agree that Vedder's decision to pull back from megastardom was crucial. His wasn't just a panicked reaction to incidents like the girl in the car, but also the result of pragmatic thinking. As other bands toppled around them, Vedder realised that carrying on as they had been doing would kill the group. Scaling down, and setting their sights a bit lower could mean survival even if it meant what even the band thought were "unpopular decisions."

"We'd gone from opening up for a hundred people at the Central Tavern to fielding phone calls saying, 'Keith Richards wants to play with you,'" says Ament. "The kid in you thinks, 'How can we say no?'" But after Vedder's persistence, they did say no – to videos, to heavy promotion, to constant touring – before their second album was released. After making increasingly wilful records, they've even dispensed with record companies, too. (Their new single The Fixer is released on their own label in the US, as will be their new album, though both are licensed to Island in the UK).

It must be said that what Rolling Stone magazine described as Pearl Jam "destroying every aspect of their success" has hardly left them penniless. Though they have had mis-steps as well as triumphs , they're still filling arenas and headlining festivals. With The Fixer getting more attention from radio than anything they've done for years, they're even on the fringes of fashionability.

They feel "empowered" to operate outside the system – like the hardcore punk bands and indie labels they followed as kids – though it's not so punishing to do that when you've already sold 60m albums. As Vedder says: "Bands like [DIY punk stalwarts] Fugazi make us look like Mariah Carey."

Nevertheless, it's just part of a long tradition the band have of kicking against the music industry. Ament describes their most confrontational decision – to take on the powerful ticket agent Ticketmaster in 1994 over concert prices – as "career suicide". They cancelled their summer 1994 tour rather than allow Ticketmaster to set prices they did not approve. Because of Ticketmaster's close links with the US arenas, Pearl Jam were persona non grata at many major venues, and put on their own shows.

"We'd be ­ playing parks and racetracks," Ament says. "And somebody would be yelling, 'The fence is down a mile in the east corner!' and we'd have one guy trying to fix it. It was absolutely stupid." The band gave evidence to a congressional hearing on ticket prices, and when nothing came of it, they launched their own lawsuit against Ticketmaster. Ament says it felt like they'd taken on "the whole of corporate America". They lost, were working with Ticketmaster again within four years, and Vedder admits things are even more corporate now. But he thinks Pearl Jam's willingness to take stands that damage themselves means "people trust us. They get the feeling this means something".

Pearl Jam do not take their role lightly. When nine people died in a stage crush during their set at Roskilde in 2000, they retired from festivals for six years. The incident makes for difficult conversation. "When we stopped the show, there were people down," says Cameron. "Within a minute, bodies were being passed over the barricades." Ament can't comprehend how a rock concert became a "disaster". Vedder can't talk about it at all. "I'd never make it," he says, softly.

These days, the singer pours his anger into political campaigning. He insists that unlike the Dixie Chicks, Pearl Jam didn't lose fans after criticising the Bush administration, though they "didn't win any either". He's still furious about the last presidency. "Those fucking bastards, they put us in this situation and screw up the whole fucking planet and goodwill with every other nation, and they are not going to be held criminally responsible."

Above him in the HQ there's a portrait of Obama. Vedder concedes that things are changing, but there's so much that hasn't: "People on death row, the treatment of animals, women's right to choose. So much in America is based on religious fundamentalist Christianity. Grow up! This is the modern world!"

He sounds more like an angry kid than a middle-aged man. He sounds as contrary as one, too. The new album, Backspacer, is a return to Ten's worldbeating rock sound – but maybe Pearl Jam will follow it with an album of Crass covers. The band are only "halfway through" their career, Vedder says, and perhaps these grunge warriors wouldn't know what to do if there was no more fighting. When I ask Vedder what he'd do if Pearl Jam ended tomorrow his reply is dramatic, pragmatic and defiant.

"I'd take my guitar with me."

Pearl Jam play MEN Arena, Manchester on Monday, and the O2, London, on Tuesday. Details: livenation.co.uk. The Fixer is out on Island on 7 September, followed by Backspacer on 21 September.