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Did The New York Times bury stories that cast doubt on Bush’s Iraq War push?

At The Intercept, former Times investigative reporter James Risen asserts that the paper’s editorial leadership had squashed stories critical of the Bush administration’s line on Iraq:

What angered me most was that while they were burying my skeptical stories, the editors were not only giving banner headlines to stories asserting that Iraq had weapons of mass destruction, they were also demanding that I help match stories from other publications about Iraq’s purported WMD programs. I grew so sick of this that when The Washington Post reported that Iraq had turned over nerve gas to terrorists, I refused to try to match the story. One mid-level editor in the Washington bureau yelled at me for my refusal. He came to my desk carrying a golf club while berating me after I told him that the story was bullshit and I wasn’t going to make any calls on it.

Risen also claims that the administration exerted direct pressure on the Times to bury a major scoop on the NSA’s post-9/11 surveillance in the name of protecting national security. In Risen’s account, editor after editor accepted the Bush administration’s rationale almost entirely uncritically. But the problem wasn’t limited to the Times:

That fall, I became so concerned that the Times would not run the NSA story and that I would be fired that I secretly met with another national news organization about a job. I told a senior editor there that I had a major story that the Times had refused to run under pressure from the White House. I didn’t tell him anything about the story, but I said if they hired me, I would give the story to them. The senior editor replied that their publication would never run a piece if the White House raised objections on national security grounds. I left that meeting more depressed than ever.

The Times did eventually publish the story, a delayed decision that enraged the Bush White House and led to an investigation of Risen’s sources. Things didn’t improve under Bush’s successor. The Obama administration also pursued Risen’s sources for another story on the CIA’s Operation Merlin in Iran; Risen says they used the case to “destroy the legal underpinnings of the reporter’s privilege in the 4th Circuit.”