The incident prompted Globe editor Martin Baron to publicly disassociate the paper from any libel threat. But he said the Globe will continue to work with the Center, calling it an “evolving relationship.” “I’ve made clear publicly that we are not a part of that incident,” Baron said. “People do things we don’t approve of all the time, sometimes on our own staff. No one incident would cause us to disassociate from someone.” Baron said the two organizations are working through structural questions about how stories are handled. For example, Baron signaled that he doesn’t much like being forced to run a story on a particular day because other publishing partners are doing so. “We like to work on our own schedule,” he said.

Other sites have had hiccups, but so far, big blowups have been avoided, despite the speed and multi-tentacled process by which sensitive stories are being handled. For instance, no one has yet suggested that any site secretly takes money to promote a funders’ political or policy agenda, something some investigative journalists worry could happen in the philanthropic model. The Investigative News Network, in fact, specifically excludes members that don’t publicly disclose all donors on their Web sites.

How far the influence of donors and their causes will creep into stories is being watched closely. “For investigative startups that depend on benefactors, it certainly is possible to see a time when the interests of the benefactors come into conflict with the inquiries of the journalists,” said Duvoisin of the Los Angeles Times. “I’m confident the editors at these organizations can manage potential conflicts, but it may take vigilance over time as this plays out. One shouldn’t assume nonprofit equals independent. It’s much the same battle journalists have fought for years to preserve their independence.”

Jeff Leen, who heads the investigative team at The Washington Post, is not worried that donor influence will produce slanted reporting or unjustified conclusions, because investigative projects get such scrutiny. “The hardest thing is to get your investigation noticed,” Leen said. “To do that, you have to have the goods.” No amount of hype or slick presentation can cover over thin investigative reporting, he said. “If it’s not any good, the whole project just drops down a deep well.”

Leen compared the path of investigative reporting to that of Hollywood. In the old days, studios controlled the process: they employed the writers, the actors, the producers, the designers. Today, studios produce some of their own films, but there’s also a thriving pool of independent producers who pitch their ideas to the studios. “You have to make a lot of movies to get a few good ones,” Leen said, adding that he welcomes both the competition and the collaboration with these new independent investigators.

Besides, Leen added, the nonprofits are employing many friends and journalists he deeply admires, who were forced to leave their newspaper jobs.

Can it last? At California Watch, Freedberg believes that his group is creating something that will endure beyond a few funding cycles. “We’re on this innovation curve, going in an upward direction, as opposed to a survival curve,” he said. But they’re taking nothing for granted. When editors realized too late that their big story on university building safety was going to run during spring break, they turned to a time-honored tradition to get the news out: as the U.C. Berkeley students streamed back the following week, Katches and other California Watch staffers stood outside their office near campus and distributed fliers advertising the story. “It’s all about getting stories into the hands of people who are impacted by our journalism the most—one at a time, if need be,” Katches wrote in a blog item.

Indeed, the need to investigate the bastards runs deep. Rosenthal describes how he was hooked. Stuffed between his desk and a glass wall in his cluttered California Watch office is a heavy-paper mat, made with the impression from the printing-press plate of the front page of the June 13, 1971 edition of The New York Times. The lead story: the Pentagon Papers, a piece drawn from the secret history of the war in Vietnam as compiled by the U.S. Department of Defense. In one of his first assignments as a Times copy boy that year, Rosenthal was assigned to the secret Hilton Hotel team that was combing through the documents, looking for sections to describe and publish. He slept in the room with two filing cabinets that held the Pentagon Papers, and got to Xerox several parts of them. The reporters and editors, he said, accepted him as part of the team.

So began a glorious adventure into investigative reporting of the highest caliber. And it ain’t over yet.

Jill Drew is a 2009-2010 Encore Fellow at CJR. She was an associate editor at The Washington Post until August 2009. For nine of her fourteen years at the newspaper, she was assistant managing editor for financial news.