Dr. Keller of Redeemer Presbyterian has built his ministry very much on confronting the challenge. His books include “The Reason for God: Belief in an Age of Skepticism.” He periodically teaches an adult-ed class titled “Questioning Christianity” and sometimes holds question-and-answer sessions with attendees after Redeemer’s Sunday worship services.

His decision to open a branch of Redeemer on West 83rd Street in 2012 — the first new church built in the neighborhood in decades — was a brick-and-mortar way of meeting nonbelievers where they live. And he prepared his young ministers and staff members for the Upper West Side by studying together such books as the philosopher Charles Taylor’s “A Secular Age.”

On that recent Tuesday evening, Mr. Ellis, the pastor’s assistant, was sharing a lectern with the Rev. Bijan Mirtolooi, the assistant pastor for the 83rd Street church. In the chairs around them sat people like Frank Ying, 33, who works for a technology start-up. Brought up in the Dallas area by immigrant parents who had been raised amid the official atheism of the People’s Republic of China, Mr. Ying tried exploring Christianity with his high school classmates, even accompanying them to megachurches, only to be put off by their fundamentalism.

“You have all these questions,” he recalled. “And you have all these long, drawn-out conversations. ‘What do you believe? How much of the Bible do you take literally?’ And these people stop short and say, ‘You’ve just got to have faith.’ But I’ve always been more pragmatic, so that wasn’t good enough.”

Mr. Ying heard about Redeemer Presbyterian from a few acquaintances after moving to Manhattan several years ago. He dipped his toe slowly, watching a YouTube video of Dr. Keller in conversation with a journalist and a historian, emissaries of the secular world. By now, Mr. Ying is a regular at the WS Café, not because he believes, but because his doubts get heard.

Each session has a central topic, and on the recent Tuesday it was about why Jesus needed to be crucified. As part of framing a wide-open conversation, a list of quotations on the subject even included this zinger from Mr. Hitchens: “I find something repulsive about the idea of vicarious redemption.”

Mr. Ellis and Mr. Mirtolooi cited popular culture (movies like “The Revenant,” “Inside Out”) and real-life examples (the way a parent sacrifices free time to raise a child) in order to make palpable the concept of suffering leading to the remission of sin. Very deliberately, they did not lean heavily on Scripture.