In a companywide meeting last week, New York Times Managing Editor Joe Kahn fielded a question about Andy Mills, the prominent audio producer who has worked on popular podcast “The Daily” and played a leading role in the failed 2018 podcast series “Caliphate.” Though Kahn couldn’t part with details, he did say, “Please don’t mistake silence for inattention and inaction.”

Now action has arrived. After reports earlier this week that his Slack account had been deactivated and his email address was not working, on Friday afternoon came the news that he’d resigned.

“Today I’m resigning from The New York Times. Those are not words I ever wanted to write,” wrote Mills in a note posted to his website. But as reported previously here, Mills’s career came under scrutiny in late December, following the Times’s announcement that it had bailed on “Caliphate,” key episodes of which rested on a Canadian man whom authorities later charged with conducting a terrorism hoax. Mills shared top billing on the series with star Times reporter Rukmini Callimachi. Callimachi was reassigned to a new beat — higher education — on account of “Caliphate.” Just days after the announcement, however, Mills co-hosted an edition of “The Daily” — sparking questions as to whether Mills had escaped accountability while Callimachi received a very public change of beats. Along with that sentiment came a recirculation of allegations regarding his treatment of female colleagues in a previous posting at WNYC’s “Radiolab.”

In the case of Mills, it wasn’t just Twitter users who were pounding the newspaper. Public radio stations that carry “The Daily” sent a letter to the Times raising concerns about how it apparently allowed Mills to skate free of accountability. "We feel your decision was not just tone-deaf, but blind to the current landscape in which we now exist,” reads the letter. Assistant Managing Editor Sam Dolnick responded quickly that the newspaper investigates all allegations of misconduct and that the timing of the Mills-hosted episode was a “mistake.”

Mills wasn’t the only Times journalist to depart under a cloud this week. A Daily Beast report last week revealed that science reporter Donald McNeil had been accused of saying racist things during an educational trip to Peru with students in 2019. “We conducted a thorough investigation and disciplined Donald for statements and language that had been inappropriate and inconsistent with our values,” said a Times statement, in part. After pressure from Times staffers, the paper announced on Friday that McNeil had resigned.

In his resignation letter, Mills inventories his past, admitting to mistreatment of colleagues in his former posting. “Like all human beings, I have made mistakes that I wish I could take back,” writes Mills. “Nine years ago, when I first moved to New York City, I regularly attended monthly public radio meet up parties where I looked for love and eventually earned a reputation as a flirt. Eight years ago during a team meeting, I gave a colleague a back rub. Seven years ago I poured a drink on a coworker’s head at a drunken bar party. I look back at those actions with extraordinary regret and embarrassment.”

That regret and embarrassment come mixed with resentment toward people on Twitter. “The allegations on Twitter quickly escalated to the point where my actual shortcomings and past mistakes were replaced with gross exaggerations and baseless claims,” he writes. “Several people have even alleged that I am a predator and a dangerous threat to my colleagues. I have been transformed into a symbol of larger societal evils. As a journalist, it has been especially discouraging and upsetting to see fellow journalists make such claims or retweet them.”

As for the breakdown of “Caliphate,” Mills writes that newspaper leadership had declared that “they had their own internal system in place for stories of this nature. That system broke down. And they did not blame us.” In addition to the reflections in his departure letter, he hints that there may be more revelations to come: “At some point, maybe I’ll tell this story more fully, but I got into this work to tell other people’s stories. And for now, I’m going to get back to that,” he writes.

Read more from Erik Wemple: