William Lynch was brimming with the enthusiasm of a start-up entrepreneur. It was January 2012, and Mr. Lynch, Barnes & Noble’s chief executive, was showing off the company’s shiny Palo Alto, Calif., offices, a 300-person outpost that was the center of its e-reader operations.

He and other executives proudly displayed their new devices, talked about plans to expand and promised that the bookstore chain could go head-to-head with the giants of Silicon Valley.

“We’re a technology company, believe it or not,” Mr. Lynch said.

But only 16 months later, Barnes & Noble’s digital plans are crumbling. Last month, a disastrous earnings report coincided with the company’s announcement that it would no longer manufacture color tablets. And on Monday, Barnes & Noble announced that Mr. Lynch, the young, tech-savvy architect of the company’s digital strategy, had abruptly resigned. A new chief executive was not named.

That leaves the nation’s only major bookstore chain without a clear path forward, reviving fears among publishers, authors and agents — who are deeply dependent on a viable Barnes & Noble — about its future.