According to sources, Coker’s departure stemmed from a bizarre set of run-ins with her colleague Rukmini Callimachi, a Times reporter who since 2014 has attained larger-than-the-Times stature for her coverage of al-Qaeda and the Islamic State.

The problems started when Callimachi and a video team planned to film an episode of “The Weekly,” a documentary series stemming from a partnership between the New York Times and cable channel FX. The group landed in Erbil, Iraq, but Callimachi was denied entry into the country.

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It’s no surprise that Callimachi might encounter border difficulties with Iraq.

A Callimachi’s investigation titled “The ISIS Files” appeared in the New York Times in April, drawing from 15,000 pages of documents gathered over five trips to Iraq. The papers showed just how the Islamic State ruled its caliphate. Awkwardly and brutally, as it turned out. Highlighted in the investigation was the story of Ibrahim Muhammad Khalil, a 14-year-old who was arrested in 2015 by Islamic State police after “laughing during prayer.” Scholars questioned the propriety of gathering and removing so many documents from Iraq.

Iraqi officials weren’t pleased with the goings-on, either. Iraq sent a May 24 letter to Coker herself requesting the return of the documents and a formal apology from the newspaper. The newspaper eventually did return the documents.

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According to informed sources, Coker wound up under suspicion for tipping off Iraqi officials to Callimachi’s arrival with the video crew. The Times interrogated Coker at length about the matter and requested her electronic communications in search of evidence that she had acted appropriately as bureau chief. Leadership at the Times concluded that Coker had essentially colluded with the Iraqi government in barring Callimachi from the country, according to a well-placed Times source.

Also part of the Times’s investigation was the May 24 letter from the Iraq government expressing displeasure with Callimachi’s document recovery. The paper’s management concluded that Coker, disenchanted with Callimachi’s work, had played a role in prompting the government to issue the letter, according to a source at the newspaper.

Coker denied the New York Times’s claims, sources say — especially any suggestion that she’d acted in bad faith. In response to an email seeking comment, Coker wrote, “I am not in a position to comment on communications between the New York Times and me.”

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Personnel disputes this bitter don’t germinate in collegial soil. Some foreign correspondents and other reporters at the newspaper have had a standoffish relationship with Callimachi stretching back for at least two years. A multiplatform star, Callimachi has a podcast — the Caliphate — a huge Twitter following that she stokes with massive threads on terrorism and endless publicity, including an appearance on “Late Night with Seth Myers.” She is free to roam the world and turn in the longform journalistic heaves that are so valued at the New York Times.

Meanwhile, bureau chiefs are left to the whims of the news cycle, not to mention logistical challenges such as managing visas, the bureau staffs and so on.

Tensions between Coker and Callimachi also arose over ground-level matters. According to sources, Coker recoiled at Callimachi’s approach to deploying support staff at the Baghdad bureau. In vacuuming up documents for the Islamic State bureaucracy story, Coker felt, Callimachi allowed the staffers to enter dangerous places without first getting the all-clear from security personnel, said sources familiar with their dispute. A Times source disputes any such notion, insisting that the paper’s security protocols were followed in all instances.

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Like others at the New York Times, Coker thought Callimachi pushed boundaries in pursuing her stories, according to sources. She, for instance, was a key force behind obtaining a video for a February 2018 story with four bylines — Callimachi’s being the first — on how a clash with militants in the Niger desert ended in the deaths of four U.S. soldiers. The story contained this disclosure of an unusual transaction:

Helmet-camera footage from Sgt. Jeremiah Johnson was apparently seized by the militants after his death. It was later provided to a news agency in Mauritania, the Agence Nouakchott d’Information, or A.N.I. The New York Times, seeking details that would help explain how the attack occurred, bought rights to the video from the news agency last month. (A.N.I. said it did not make any payment to obtain the video.) Times reporters, working with a digital forensics expert, were able to verify the video’s authenticity and piece together the final stages of the attack. But because the video shows the deaths of the service members and also includes packaged Islamic State propaganda footage, Times editors decided not to publish the video itself.

The newspaper’s decision to buy those video rights touched off a debate within the New York Times as to whether the paper should open its wallet for any such content. The newspaper itself had previously published a story noting “suspicion” that the Agence Nouakchott d’Information had served as a tool for “dispensing terrorist propaganda,” though one analyst said there are “far worse” outlets. And an April 2017 story in which Callimachi shared a byline said ANI “is associated with Al Qaeda’s branches in Africa.” The headline read, “Website With Qaeda Ties Publishes Claim on St. Petersburg Bombing.”

As for who’ll replace Coker in Baghdad, that’s not clear at the moment.