“We would never have opened in a million years if our local bookstore hadn’t closed,” Ms. Straub said. “As a bookseller and a writer, I understand the importance of stores like Barnes & Noble. I have no interest in talking smack about the chains. But an independent bookstore is all about understanding your customers and giving them what they need. It needs to be of its place and for its place.”

Starting an independent bookstore in a borough with few book-buying options might seem like a giant leap of faith, but for Ms. Santos of The Lit Bar, it’s the culmination of a dream begun three years ago when she learned that the local Barnes & Noble would close. “Being an avid reader, that spoke to me on personal level,” she said. “While I appreciated Barnes & Noble when it was there, you would never know that you were in the Bronx. It didn’t offer a lot of opportunities for the community. If you were a local author, good luck in getting your book on the shelf. But with an independent store, you can feel the energy of the neighborhood reflected in the choices. I couldn’t think of a better way for people to engage and become real neighbors.”

There’s a difference between surviving and thriving for some indies. “Thriving is a tough word,” said Christine Onorati of Word in Greenpoint, Brooklyn (with a branch in Jersey City). “We have people who are unbelievably loyal to us, and we’re digging in, trying to make our mark, but it’s a tough business.” Rent is a challenge for many. Miles Bellamy opened Spoonbill and Sugartown in Brooklyn’s Williamsburg neighborhood almost 19 years ago, long before there was a Whole Foods and an Apple store, but he recently saw his rent almost double, to $14,500 a month from $8,000 a month.

“Just as I go to both the local drugstore and Duane Reade, book lovers can support my store and buy books online,” Mr. Bellamy said. “I feel like a better person when I go into the small store. But the pressure is constant. It’s a full-time hustle.”

There is an opportunity for certain industries to reinvent themselves after a large shock in their business model or in technology, according to Ryan L. Raffaelli, assistant professor at Harvard Business School, who has been studying independent bookstores for about five years. (He even took a course in how to open one.) “What I’ve found is that the indies are able to compete on several dimensions,” he said. “One is community. They championed the notion of ‘shop local’ and ‘Small Business Saturday.’ Another is curation: They’re not just offering best-sellers but diamonds in the rough. They’ve taken back a sense of pride in what they can provide: a deeper and ongoing relationship with their customers. In high-rent districts, because profit margins are relatively thin, success must come from multiple repeat customers, so that the customer can’t imagine not visiting as part of his or her monthly routine. They’re also flirting with adapting newer forms of technology.”

That’s what Mr. Neller is banking on. Each of the planned new Shakespeare and Company stores will have an Espresso Book Machine (Mr. Neller is also head of the manufacturer, On Demand Books) that has the potential to print and bind any book not on the shelves while you’re having a cappuccino at the store’s cafe. (Since Mr. Neller is the former chief executive of Dean & DeLuca, the new stores will definitely have baristas and snacks.)

“It’s really a renaissance,” he said, “a new permutation that will have elements of the mom-and-pop blended with technology, allowing a store to have a practically infinite selection in a small setting. We’ll take a digital file and convert it into an analog product, putting the warehouse inside a small footprint. That’s transformative.” It’s almost like a new happy ending to “You’ve Got Mail.”

Somewhere, Nora is smiling.