Warning: This story contains references to disturbing accusations and incidents of child sex abuse.

Last Oct. 18, Rolling Stone served up a foreboding scoop: The FBI had raided the home of a renowned journalist at the top of his game months earlier, and he had disappeared from public view.

It should have been a coup. Instead, acrimony inside the newsroom over how that scoop was edited led to accusations that the magazine's brash leader pulled punches in overseeing coverage of someone he knew. The reporter who wrote the story, enraged, accepted a position at a sister publication two months later. And her complaints prompted a senior attorney for the magazine's parent company to review what happened.

FBI raids on journalists are rare. News organizations often respond with formal protests and legal challenges. Under a 2021 Justice Department policy, raids, subpoenas and other compulsory means of obtaining materials from reporters are banned for any investigation of matters related to their journalism. The policy became the basis for a significant shift in the stance of the Justice Department toward the press.

The Rolling Stone story created a stir. Reporter Tatiana Siegel stated that the April 22 raid was "quite possibly, the first" carried out by the Biden administration on a journalist.

In this case, the journalist was ABC News national security producer James Gordon Meek. A former investigator for the U.S. House Homeland Security Committee, Meek had been with ABC News since 2013. He also was a producer of 3212 Un-Redacted, an investigative documentary that streamed on Hulu.

As published, the Rolling Stone article's first two paragraphs lionized Meek's record and swashbuckling style.

"Meek appears to be on the wrong side of the national-security apparatus," it stated.

As the story noted, Siegel's sources told her "federal agents allegedly found classified information on Meek's laptop during their raid." Siegel reported that Meek left his job at ABC after the raid; a publishing contract with Simon & Schuster evaporated.

As edited by Rolling Stone Editor-in-Chief Noah Shachtman, however, the article omitted a key fact that Siegel initially intended to include: Siegel had learned from her sources that Meek had been raided as part of a federal investigation into images of child sex abuse, something not publicly revealed until last month.

Why did Rolling Stone suggest Meek was targeted for his coverage of national security, rather than something unrelated to his journalism?

Neither Siegel nor Shachtman would comment for this story. This article is based on a review of some contemporaneous communications and also interviews with 10 people with knowledge of incidents described here, including several individuals at Rolling Stone, as well as people at ABC and federal law enforcement agencies.

Each asked not to be named because they were not authorized to disclose these matters publicly.

Disbelief over the nature of the accusations against a journalist

The raid on Meek's apartment occurred in April but did not become public knowledge. In September, Siegel learned details of the raid from Meek's neighbors, yet she felt the story was languishing. At a staff meeting late that month, Shachtman asked her what she was working on. She reminded him.

The next week, Shachtman stepped in to edit Siegel's story. It was rare for him to do so for her work.

As a longtime national security reporter himself, Shachtman has periodically expressed to colleagues at various outlets his skepticism of the veracity of government sources. When Siegel detailed the seriousness of the allegations against Meek, Shachtman warned her against turning in a story that included the words "child pornography" in it.

According to two people with knowledge, Mark S. Zaid, a Washington attorney who often handles national security matters and represents government whistleblowers, called Shachtman on Meek's behalf while Siegel was preparing her story. Zaid previously represented the Daily Beast on Freedom of Information Act cases while Shachtman was editor of the site.

Zaid confirms that he called Shachtman, and he tells NPR that Meek was a longtime friend and client on Freedom of Information issues. Zaid says he was representing Meek on any possible prosecution or investigation of his potential possession of classified material.

The accounts given by the associates, colleagues and friends of the two key figures — Siegel and Shachtman — diverge here. According to what Siegel told others, Shachtman and she agreed that the article would reflect that the FBI's interest stemmed from concerns of possible criminal behavior outside the scope of Meek's work — that is, it had nothing to do with national security or journalism.

Shachtman later told others that he did not believe that she had nailed down her sourcing adequately. Rolling Stone parent company Penske Media notes that authority to make such choices for Rolling Stone's coverage lies with Shachtman. "That was true in this case, as reflected in the final edits to the story," the company said in a statement to NPR. "Some material was added late in the process, other material was dropped."

In a note posted on a newsroom-wide Slack channel reviewed by NPR, Shachtman asked photo staffers to come up with a generic photograph rather than a picture of Meek. "let's not use a picture of the guy in question, james gordon meek," Shachtman requested, eschewing capital letters, in a post stamped "NEEDS PHOTO." "something FBI-y, please."

The large lead photograph shows federal agents nearing a crime scene tape in 2018 in California, with the agency's initials in vivid yellow letters on the agents' blue windbreakers.

As the two of them worked to finalize the piece, Siegel was pulled away to help care for her ailing mother. Shachtman promised Siegel he would ensure the story would land safely while she tended to her family's needs. (Siegel's mother died hours after the story was posted.)

Penske Media cites Siegel's need to deal with a family emergency as a complicating factor but says the two "were in contact up until the final moments before publishing."

In the hours leading up to publication, Shachtman changed Siegel's draft to remove all suggestions that the investigation was not related to Meek's reporting. He left in the finding that federal agents had allegedly found "classified information" on Meek's devices.

The article left many readers with the distinct impression that the investigation was linked to Meek's reporting — which could lead to a clash of the government and the press. Rolling Stone's official Twitter account promoted the story this way: "Exclusive: Emmy-winning ABC News producer James Gordon Meek had his home raided by the FBI. His colleagues say they haven't seen him since." The tweet's thrust was echoed by WikiLeaks, Glenn Beck and the Freedom of the Press Foundation, which wrote, "If this was related to his work, as this @RollingStone report suggests it might be, it is a gross press freedom violation."

On Feb. 1, the Justice Department unveiled criminal charges against Meek related to images of child sex abuse. Among other accusations, authorities say Meek shared a video showing the rape of an infant. Meek has pleaded not guilty and currently sits in federal custody.

Colleagues and friends say Siegel said she didn't know of the changes to her story until after it appeared online. Associates characterize Siegel as infuriated by what she considered Shachtman's interference in the independence of her reporting.

"The Meek case was a particularly complex one, and the editorial choices made while covering it weren't always simple or easy," Penske Media said in its statement. "So Rolling Stone stuck to a simple principle: publish in the moment as much information as it could confidently substantiate."

Rolling Stone has faced tough fallout previously from stories that did not receive sufficient editorial scrutiny. It paid millions of dollars in a series of settlements of defamation lawsuits filed over a retracted 2014 article that purported to describe a gang rape at the University of Virginia. After Columbia Journalism School completed an investigation commissioned by Rolling Stone, the school's dean at the time described a "systematic failing" inside the newsroom.

In its statement, Penske Media said that as editor-in-chief, Shachtman "makes the final call on the use of anonymous sources and background material." It noted that the magazine posted Siegel's subsequent stories about Meek, including the revelation in December — two months after the original story — that the Justice Department was preparing an indictment unrelated to Meek's work for consideration by a grand jury.

An editor who travels in the same professional circles as his story's focus

The incident cuts against Shachtman's well-cultivated image as a fearless steamroller. "Rolling Stone's at its best when it's both celebrating great art and taking down bad actors," he told The New York Times in July 2021 upon his appointment to lead the magazine. Shachtman has his own rock-and-roll cred as a professional bass player for ska bands before breaking into the top ranks of journalism several decades ago.

A month after he took over, an October 2021 Rolling Stone story titled "Eric Clapton Isn't Just Spouting Vaccine Nonsense—He's Bankrolling It" served notice that Shachtman wouldn't look away from rock icons just because they had been featured on the magazine's past covers.

Yet Siegel asked corporate officials whether Shachtman's familiarity with Meek affected his judgment on her story.

Prior to Meek's arrest, Shachtman considered Meek a peer with whom he was friendly, according to associates.

Shachtman has told colleagues that the two men travel in the same professional circles.

Shachtman boasts his own distinguished record as a national security journalist. Earlier in his career, he founded and led the national security blog Danger Room for Wired magazine. In 2010, the writer Spencer Ackerman referred in a post on the blog to "our friend James Gordon Meek." Shachtman later worked for Foreign Policy magazine before becoming the No. 2 editor and then editor-in-chief at the Daily Beast.

Shortly before Shachtman joined Rolling Stone, Meek suggested on Twitter that Shachtman should pay attention to an obscure band from Niger — the location of the botched military mission that Meek helped investigate for ABC. Shachtman replied by linking to an earlier review.

Meek soon emailed Shachtman to gauge interest in covering his Hulu documentary series. The new Rolling Stone editor passed the note along to colleagues; the magazine posted a glowing review some weeks later, in November 2021.

A takedown in the Daily Beast — Shachtman's former site

A week after Siegel's scoop ran in October, the Daily Beast's Lachlan Cartwright wrote a piece undercutting it. Cartwright's article said that the Rolling Stone piece "read like a Tom Clancy thriller and raised serious concerns that the feds raided a journalist over his work" but that sources at ABC "poured cold water" on the article's apparent premise.

Shachtman updated Siegel's story so it bore the same date — Oct. 24 — and cited the Daily Beast's story in quoting a Justice Department official saying that the department "strictly adheres" to its policy prohibiting such investigations of journalists over newsgathering.

"After the story ran - and as Tatiana's family emergency continued - Noah added a quote from a Justice Department spokesperson to the piece without consulting Tatiana," Penske Media's statement to NPR says. "He takes responsibility for that."

Siegel told friends she felt she was being mocked by one of Shachtman's former colleagues. (In his first memo upon being promoted to the Daily Beast's editor-in-chief in May 2018, Shachtman shared news of Cartwright's hiring at the digital news outlet.)

A Nov. 16 Rolling Stone article about Meek by reporter Tim Dickinson cited the Daily Beast for that Justice Department quote, as though Siegel had not earlier secured the same information about the Justice Department's policy.

In December, Siegel broke the news that the indictment was looming. By the end of that month, she was gone to Variety to serve as its executive editor of film and media. Penske Media, which owns both magazines, says the move "had been a conversation for many months–well before the first Meek story ran."

It had been a conversation, Siegel told friends in December, but she said she had decided to accept the offer only in the days before.