Eric Bates had an unusual start to his day Tuesday.

Bates is the executive editor of Rolling Stone, and his magazine was about to publish a big story outlining, with plenty of juicy quotes and telling details, the disdain—some might say insubordination—with which the military brass in Afghanistan views top civilian officials. The issue containing the story was set to hit early newsstands in major cities Wednesday. The story itself was scheduled for online publication that same day, and Bates was also set to appear on MSNBC’s Morning Joe on Wednesday.

Instead, at about 6:30 Tuesday morning, his phone rang. It was a producer for the show, asking if they could send a car for him in twenty minutes.

There must have been a mix-up, Bates said—he wasn’t due to appear for another day. “Oh, you don’t know?” came the reply.

What Bates didn’t yet know, of course, was that Gen. Stanley McChrystal, the top commander in Afghanistan, had publicly apologized for his remarks, that a furious White House had summoned McChrystal to Washington for a meeting with the president, and the story was driving both the news cycle and real-world events—before it was ever published, online or in print, by Rolling Stone.

The wheels were set in motion when the magazine provided a pre-publication copy to the Associated Press, as it does customarily, to drum up media interest and allow the wire service to do its own advance reporting. The AP’s Monday story, focusing on McChrystal’s criticisms of Karl Eikenberry, the U.S. ambassador to Afghanistan, did catch the attention of the press, and Rolling Stone was soon fielding requests for advance copies from other major news outlets. It also caught the attention of top officials, and, while the magazine had expected a significant response—“I couldn’t imagine that there wasn’t going to be a furor over it,” Bates said—the timeline moved more quickly than it had anticipated. (Rolling Stone did not provide advance copies to anyone in the White House or McChrystal’s circle, Bates said.)

So when Bates got to Rolling Stone’s offices at about 9 a.m. Tuesday, he decided that the story had to go up online immediately. It wasn’t as simple as hitting “publish” though—the online version had to finish being prepped, and, as he put it, “our day doesn’t start at 9 normally.” That meant it was about 11 a.m. when the story appeared on Rollingstone.com—the first time readers could obtain a “legitimate” copy of the story, in any format.

By that point, though, the Web was abuzz with links to two other places where PDFs of the story had been uploaded—first at Politico, and then “The Page,” Mark Halperin’s hyperactive politics blog for Time.com. Rolling Stone spokesman Mark Neschis said neither Politico nor Time.com had obtained a copy directly from Rolling Stone, nor had they requested permission to post the story.

When Bates learned that the other sites had posted the article, he moved “with great dispatch” to request that the files be taken down, which they promptly were. (A spokeswoman for Time.com declined to comment. John Harris, Politico’s editor-in-chief, confirmed in an e-mail message that the PDF was pulled down at Rolling Stone’s request, but did not explain the site’s thinking in originally posting the story.)

In an interview this afternoon, Bates was critical of the other sites’ decision to post the PDF. Even without the ability to link to the story on Rolling Stone’s site, he said, posting the embargoed copy to their own site is “not permissible.”

“It doesn’t matter how big a story it’s become—that’s our decision” about when to publish, he said. “That’s not somebody else’s decision to make for us.”

Could the publication by other sites be viewed as a reasonable response to a perceived information vacuum at the center of the day’s biggest story? In response to the intense interest, Rolling Stone moved as fast as it could to get the story up Tuesday, Bates said. And if that wasn’t until mid-morning? “Oh my God—for a couple of hours, nobody could read it.”

Leaving the ethics of publication by other sites aside, some observers are questioning whether Rolling Stone missed an opportunity to capitalize on its story. With the wave of perfectly legitimate commentary, discussion, excerpting, and follow-on reporting that the story generated, it wasn’t until late Tuesday afternoon that the original story even showed up on the first page of results for the Google search “mcchrystal rolling stone.” That had Business Insider’s Joe Pompeo asking, “Did Rolling Stone Just Massively Blow its own McChrystal Scoop?”

Greg Marx is an associate editor at CJR. Follow him on Twitter @gregamarx.