On Aug. 27, a fairly straightforward obituary about Ted Kennedy for the Web site was subjected to a little political re-education on the way to the front page. A new paragraph was added quoting Rush Limbaugh deriding what he called all of the “slobbering media coverage,” and he also accused the recently deceased senator of being the kind of politician who “uses the government to take money from people who work and gives it to people who don’t work.”

Image Rupert Murdoch, a lifelong conservative, addressing the newsroom at The Wall Street Journal two years ago, when he took over. Credit... Mark Lennihan/Associated Press

On Oct. 31, an article on the front of the B section about estate taxes at the state level used the phrase “death tax” six times, but there were no quotation marks around it. A month later, the newspaper’s Style & Substance blog suggested that the adoption of such a loaded political term was probably not a good idea: “Because opponents of estate taxes have long referred to them as death taxes, the term should be avoided in news stories.”

In response to questions about bias in the newspaper, a Journal spokesman sent along the following statement: “The Journal has always provided its readers with unique, objective news reporting from our Washington Bureau.”

None of the reporters involved in those articles spoke to me, but several others did.

“A lot of it is about what goes into the pipeline and then what does, and does not, come out,” said a reporter who works at the Washington bureau and who, like others, did not want to be identified out of concern for retribution. The reporter said articles at The Wall Street Journal ended up looking out of step with other coverage because an agenda may have been at work.

Tension between Washington bureaus and headquarters is a common feature of newspapers, and none of the people I spoke to suggested that either Mr. Thomson or Mr. Baker lacked savvy as journalists or leaders  only that ideology was baked into the coverage through headlines, assignments and editing in a way that had never occurred in the past.

“When it was just Robert, we were able to win more arguments, but now that it is both he and Baker, it pretty much goes the way they say it will,” said another current member of the staff.