Rolling Stone magazine is still counting the cost this week of its scoop that became everyone else’s biggest story. The New York Times reports is reporting how Rolling Stone magazine failed to benefit from its story about General Stanley McChrystal last week after news websites, wires broadcasters and bloggers all took the story and ran with it.

It was a story (The Runaway General) that didn’t get much bigger. It went all the way to the very top, to President Barrack Obama’s desk, and had extraordinary ramifications resulting in the sacking of America’s top general in Afghanistan and an examination of how that war is being fought.

But while we all read about the story few actually read it on Rolling Stone’s website after it made a serious of errors in how it handled its global scoop.

It began with Rolling Stone seeding the story to AP and others (under restrictions) and then two websites, Time.com and Politico, taking the story without permission and re-producing a PDF of the entire article. Yes all of it. This meant that they had published the whole thing online before Rolling Stone (the owner of the content) for free. Publishing an entire feature article as a PDF document is not fair use that’s more like theft. It isn’t something that you expect mainstream media organisations to engage in. On their parts that is a breathtaking breach of media protocol. A publishing crime if there ever was one.

This resulted in the story being picked up everywhere, on and offline, and while Rolling Stone got lots of mentions it didn’t make a penny from any of it and it didn’t reap the rewards of the subsequent web traffic.

Both Time and Politico removed the PDFs when asked to do so and argued that they published because the piece was being widely circulated and talked about and readers had a right to see what was being talked about. That is a weak defence.

That said, I don’t think Rolling Stone has anyone to blame but itself. It had a huge story that it seeded and then that got shared around. It was too big to keep in the bag.

It’s like Emily Bell writes in The Guardian today: Rolling Stone tried to ignore the invention of the internet. It hoped instead to stoke an old fashion bumper newsstand sale. It might still get those sales, but other media organisations have reaped the online benefit. Look at the story on Rolling Stone’s website, it got only 48 comments.

In its defence Rolling Stone said that when to publish online was its and its decision alone.

Eric Bates, executive editor of Rolling Stone, told the New York Times: “This is not about our slow-footedness on the web, but our right to publish on a schedule we chose. To me, this was really a transitional moment. We’ve had fan sites that have published the text of some stories, but what these two big media organizations did was really off the charts. They took something that was in a prepublished form, sent out to other media organizations with specific restrictions, and just put it up.”

I don’t think Rolling Stone or Bates could be more wrong. The genie was out of the bottle and it gave up control of the story as soon as it began to tell people about it. This was always going to happen. The story is too big.

The incredible thing is that the reporter Michael Hastings wrote the story and filed it and it didn’t leak. It then went all the way through the production process and no one appears to have asked the question: “shouldn’t we break this on the web as its kind of really huge?”.

But then if you look at the cover of Rolling Stone and see the lack of prominence the article is given — a small coverline on the bottom left – with less prominence that just about everything else you get the impression Rolling Stone didn’t know what it had or what to do with it, which makes what happened next less of  a surprise.