After The Daily Beast’s report, Mr. McNeil told The Times he saw no reason to apologize, but within 48 hours was beginning to draft an apology, a person with direct knowledge of that document said. He exchanged a series of drafts with Times management over the next week. By Feb. 5, The Times had made clear that he would be moved to a less prestigious beat, and that he could face ongoing questions from the company’s H.R. department. It’s not surprising that he resigned. Editors forwarded his apology note, which seemed by then both uncharacteristically profuse and oddly late, in an email that announced his resignation.

The questions about The Times’s identity and political leanings are real; the differences inside the newsroom won’t be easily resolved. But the paper needs to figure out how to resolve these issues more clearly: Is The Times the leading newspaper for like-minded, left-leaning Americans? Or is it trying to hold what seems to be a disappearing center in a deeply divided country? Is it Elizabeth Warren or Joe Biden? One thing that’s clear is that these questions probably aren’t best arbitrated through firings or resignations freighted with symbolic meaning, or hashed out inside the human resources department.

The Times will have to navigate its identity in tandem with the next generation of its audience — people like Ms. Shepherd, who said that she was most surprised by the gap between Mr. McNeil’s views and what she’d read in her favorite news outlet.