The man he replaced, Mr. D’Vorkin, faced suspicion in the newsroom almost from his arrival, partly because of his previous role at Forbes, where he broadened the company’s native advertising offerings and introduced a product that allowed advertisers to contribute material alongside Forbes articles. Newsroom skeptics feared that he would focus more on clicks and advertising innovations than quality journalism.

Tronc executives decided to move Mr. D’Vorkin, 65, out of the top newsroom job at a time when they were also revisiting a companywide reorganization plan, according to two company officials briefed on the discussions. The proposal seemed intended to cut costs and increase the emphasis on making Tronc’s journalism better suited to digital media. Mr. Levinsohn, the publisher now on leave, was a main architect of the restructuring plan. But the plan is now in flux, according to the two people.

Mr. Levinsohn’s leave came at the end of an aggressive attempt by Times management to thwart the newsroom’s ultimately successful union drive — a campaign that occurred as the paper’s editors and reporters were distinguishing themselves with aggressive coverage of sexual harassment in Hollywood and natural disasters in California.

Tensions between the paper’s employees and its management team had been rising since a dispute between The Times and the Walt Disney Company. After Disney banned Times journalists from attending advance film screenings following the publication of an investigative series on the company’s ties to the city of Anaheim, some people in the newsroom questioned how Mr. D’Vorkin had handled the paper’s response.

During a staff meeting, after learning that a recording of an earlier meeting had been leaked to a New York Times reporter, Mr. D’Vorkin said that anyone involved with the act was “morally bankrupt,” according to several people in attendance. His admonition further escalated the divide between employees and management.

Several journalists at The Times said they worried that the company, eager to stanch the steady stream of reports other news organizations were publishing about it, had begun monitoring their phones and computers in pursuit of leaks. Two journalists said they had been warned that the company was monitoring employees’ emails.

In a statement, Tronc said that it was committed to respecting employees’ privacy. “There’s never to our knowledge been a situation where the company is monitoring people’s emails,” the company said.