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Faced with a renewed call last week to apologize for the 1969 raid on the Stonewall Inn, the New York Police Department proclaimed that the “N.Y.P.D. of today is much different than the department of 50 years ago.” It alluded to “important changes” made to “bring the police and all the communities we serve closer together.”

What it did not do was offer any acknowledgment of wrongdoing or regret for the raid that led to days of street protests, a seminal moment that galvanized the modern gay rights movement.

Shortly after the statement’s release, the city’s police commissioner, James P. O’Neill, had misgivings. “Through the afternoon and through the night,” Mr. O’Neill recalled, “I knew we had to do more.”

He began scribbling a full-throated apology on notecards, and kept them in his breast pocket. He told no one what he was writing, drafting it longhand, on the fly. No call to the mayor. No high-level meetings.