How did Rolling Stone magazine bring down America's top general?

Rather they are attached to a bra worn by a near-nude Lady Gaga, whose revelation that she is "terrified" of babies is the issue's chief selling point. Only after drawing its readers' attentions to features on Dennis Hopper, BP and the Bonnaroo Music Festival, does it mention the profile of McChrystal, which revealed his contempt for President Barack Obama and other political leaders and led him to be replaced by General David Petraeus.

This is the contradiction at the heart of the magazine. It explains why – despite a tradition of reportage stretching back to its 1967 launch by owner, editor and publisher Jann Wenner – the first response to the scoop in many quarters was a bemused: "Really, in Rolling Stone?"

Executive editor Eric Bates is so used to this, he calls it the "Of All Places" syndrome. "There's still this lingering sense you're a music magazine and what are you doing over in Afghanistan," he says.

But the fact that Michael Hasting's profile of McChrystal was published in this magazine will have come as no surprise to those acquainted with its history. From its inception in San Francisco during the Summer of Love, it has been associated with cutting-edge journalism in general, and in-depth pieces about the military in particular. In the Seventies, it gave birth to a new style of more subjective and flamboyant writing – known as Gonzo journalism – pioneered by its most famous contributor Hunter S Thompson, who produced a savage attack on the political system after going on the campaign trail with Richard Nixon and Senator George McGovern.

While always focusing on musicians on the cover, it broke new journalistic ground inside, with Howard Kohn's inside story on Patty Hearst's flight across the US with her abductors; and an investigation into the suspicious death of Karen Silkwood, campaigner at an Oklahoma nuclear energy plant placing it at the forefront of investigative reporting.

Even in the late Eighties and Nineties – when many critics felt it had lost its way – it carried a series of articles by Eric Schlosser which became Fast Food Nation, as well as David Lipsky's feature on the US Military Academy at West Point, the longest piece it had printed since Thompson's Fear And Loathing In Las Vegas.

Most recently, it took on the banks – with Matt Taibbi describing Goldman Sachs as a "vampire squid wrapped around the face of humanity relentlessly jabbing its blood funnel into anything that smells like money" – and nurtured the talent of Evan Wright, whose features on his time embedded with 1st Reconnaissance Battalion of the US marines during the 2003 invasion of Iraq became the award-winning book and mini-series Generation Kill.

"What Jann does is he finances a journalist to go out (on a job] for a month or two months, and he'll say take your time to write it, take your time to research it, and we'll pay you for it, we'll cover your expenses, and that's very rare," says Wright. "Even back at the invasion of Iraq, there were approximately 500 journalists embedded with coalition forces, but I was told there were only two or three of us there for the duration, given free rein."

What is more surprising, perhaps, than Rolling Stone's publication of the McChrystal story, is that the General agreed to be part of it, given its anti-establishment and left-leaning sensibilities.

Wenner has contributed to the Democrat Party and the magazine supported Al Gore, John Kerry and Obama in the 2000, 2004 and 2008 presidential elections. But although it wears its liberal credentials on its sleeve, the magazine has never been enslaved by them. "The Marine Corps gave Generation Kill this thing called the General (Wallace M] Greene Award, (because] they considered it the best piece of history of the corps. It liked my writing, so clearly Rolling Stone is capable of journalism that defies the expectations that it's a liberal magazine," says Wright. "They support the Democrats, but doesn't mean they hate the military or they are incapable of seeing good points that come out of the right."

McChrystal, once a hard-drinking, rebellious graduate of West Point, might have been attracted to this irreverence.

Its refusal to be pigeon-holed and its determination to remain outside the mainstream comes down to the idiosyncratic approach of its owner. When Wenner, the son of a baby food magnate, set up Rolling Stone with $7,500 borrowed from a relative, his vision was for a counter-cultural magazine which stood outside the mainstream, but did not embrace the radical politics of underground newspapers such as the Berkeley Barb.

Its impact was explosive and it launched the careers of the best writers of the generation. As Thompson pioneered his Gonzo style, PJ O'Rourke described his Holidays in Hell in places such as Manila, a young Cameron Crowe went on the road with rock bands, Tom Wolfe wrote the Brotherhood Of The Right Stuff (about Nasa's first seven astronauts), and Annie Leibovitz took photos for the covers, including the image of John Lennon curled up naked beside a fully dressed Yoko Ono.

By the late Seventies – when punk was the rage in the UK – its musical tastes began to seem anachronistic. Moving to New York in 1977, it lost some of its credibility when Thompson openly criticised it for turning against marijuana, despite having embraced the drug in its heyday.

Then, in the Nineties, under British editor John Needham, who made his name at lads' mag FHM, it faced accusations that it was dumbing down. But, through all this, the bi-weekly publication, which has a readership of around 1.4 million, continued to provide a platform for anti-establishment stories others wouldn't touch.

Michael Hastings' piece about McChrystal – which claimed the general's scalp before it hit the news stands and could be read elsewhere before the magazine managed to get it up on its website – is firmly in the Rolling Stone tradition.

Based on conversations between McChrystal and his aides that took place between April and mid-May, the piece shows them mocking and criticising all the senior civilians in their chain of command. In particular, aides were quoted suggesting McChrystal was "disappointed" in a meeting with Obama, sneering at vice-president Joe Biden ("Who's he?") and accusing US ambassador Karl Eikenberry – whose reticence over a request for more troops was leaked to the press – of covering his "flank" for the history books.

Hastings insists he did not set out to get McChrystal fired. "It was to get people to say: 'Hey, what's going on in Afghanistan?' It's often as if America doesn't realise it's fighting two wars."

Not everyone has lauded his work. One rival reporter in Kabul dismissed the piece as "people bitching about Washington" and a Fox commentator described him as "a rat in an eagle's nest". There have even been accusations that Hastings – who wrote How I Lost My Love In Baghdad after his aid worker fiance was blown up in a car bomb – had engaged in underhand tactics such as getting McChrystal and his aides drunk or using quotes that were supposed to be "off the record". But with McChrystal making no claims that any protocol was breached, this seems unlikely.

Wright is as surprised as anyone else by McChrystal's remarks, not because he is unused to soldiers letting down their guard, but because he sees no purpose to it in this case. "Usually when someone is trash talking or criticising the chain of command, that person will have a strategy – they will believe something is wrong and want to improve it. What shocked me about the McChrystal article is that he actually shares the same strategic objectives as the civilian leadership, as Obama. If you have the same goals as your boss why would your people be on the record making fun of them?" Wright asks. But he is adamant that, whatever McChrystal's motives, the expos resulted from Hastings having time to bond with his subjects. Rolling Stone's investment in reporters is rivalled in the US only by Vanity Fair. And its ability to mesh music and politics (and low and high culture) has never been successfully emulated in the UK, although, arguably, the style of documentary-makers Nick Broomfield and Louis Theroux is Gonzo journalism.

"I suppose you could say some style magazines of the past, such as The Face, had an interest in politics," says media expert Professor Brian McNair. "But it is true there is nothing in this country like Rolling Stone. Perhaps that's because we have well-developed broadsheet and quality newspapers which cover politics in depth. The US has the likes of the New York Times and the Washington Post, but nothing national, so maybe that explains the difference."

For Wright, however, Rolling Stone's unique format comes down, almost entirely, to its owner. "Rolling Stone came out of a tradition from the late Sixties early Seventies when people listened to music and they thought they could change the world," he says. "The presumption that Jann Wenner had was 'oh, they want to read about music and about important news because they are engaged'.

"That's not true any more. I don't think young people feel like they can change the world, and music is vapid and stupid, but Jann has clung to this ideal

. Journalism thrives in Rolling Stone because of Wenner's vision."