People involved with the discussions stressed this week that no merger agreement has been reached, and that the legal and financial logistics of combining two California nonprofit organizations, both of them regulated under section 501(c)3 of the Internal Revenue Service code, are daunting. Any merger agreement would have to be approved by the state attorney general, Kamala Harris, who oversees mergers of nonprofit corporations.

“The attorney general could step in and apply the brakes if she finds organizations proposing to merge where the missions and purposes of the two don’t match up,” said Gene Takagi, a specialist in the law of nonprofits and managing attorney at the NEO Law Group, based in San Francisco.

“If the opera and the Society for the Prevention of Cruelty to Animals propose a merger, that’s going to be a problem,” he said.

In a presentation to the Bay Citizen’s board last week, Bronstein, the leading candidate to be the combined organization’s chief executive, presented a vision of the combined news groups that would create “an unprecedented level of accountability reporting for the Bay Area” and create “the largest investigative reporting team in the region.”

However, in his presentation, Bronstein also suggested “economies of at least $1 million in operational expenses and $900,000 in duplicative personnel.” He outlined plans for the combined organizations to focus on “entrepreneurial journalism,” raising the possibility of turning the technology of the news group into a profit center.

Conspicuously absent from his presentation was the Bay Citizen’s contractual agreement to provide The New York Times with Bay Area news each week. Bronstein said the agreement could possibly conflict with partnerships that CIR has with dozens of other print partners.

What the possible merger means for The Bay Citizen, CIR and California Watch, three of California’s most ambitious public-interest reporting ventures, is a topic of intense speculation in their respective newsrooms.

“Journalists have been left out of the process,” said Aaron Glantz, a Bay Citizen staff reporter and chairman of the newsroom’s Newspaper Guild unit. “Neither the organization’s board of directors nor the outgoing CEO have ever consulted with staff on the possible merger.”

Fainaru attended several board meetings where the merger was discussed, but declined to talk about specifics. As for his departure, he said the opportunity to work on a book with his brother, the investigative journalist Mark Fainaru-Wada, “has always been a dream of ours.”

With the board unable to define its strategy, “I felt the decision was pretty much made for me,” Fainaru said. He told colleagues that he would also take an investigative journalism job with ESPN. His last day is Thursday.

“We are deeply concerned that in the absence of a CEO and editor-in-chief, we do not have an advocate who will fight for what we have all worked so hard to build here at The Bay Citizen,” Glantz said in an e-mail.

Robert Rosenthal, executive director of CIR, said: “I think there’s a tremendous possibility of bringing together two strong and unique organizations and blending their strengths and assets into something unique in nonprofit journalism. It could be transformational in terms of innovation around story delivery on all platforms and engaging its audiences in ways that were unthinkable even five years ago, as the technology and social media are evolving.”

Bronstein said that he shares the same vision as Rosenthal.

He added that discussions were fluid. “Things could gel quickly,” he said, “and they could also fall apart quickly.”

This article also appears in the Bay Area edition of The New York Times.

Correction: A previous version of this article misstated Lisa Frazier's reason for resigning as CEO of The Bay Citizen. She resigned for personal reasons, she said, not health reasons. The article also incorrectly stated that California Watch had 27 editorial employees. The Center for Investigative Reporting has an editorial staff of 27, a figure that includes California Watch's reporting and editing staffs.