Twenty-five years after divers first mapped Cuba’s mysterious underwater pyramids, a new expedition finally returned—and the sonar screens went dark before the images ever surfaced. The ancient stone structures, discovered off the coast in 2001, were long dismissed as a geological fluke.

In May 2001, a marine survey team working off Cuba’s Guanahacabibes Peninsula detected unusual formations on the seafloor at a depth of roughly 2,000 feet. The team, led by engineer Paulina Zelitsky and her husband Paul Weinzweig, was under contract with the Cuban government to search for colonial-era shipwrecks. Using side-scan sonar, they located what appeared to be straight edges, circular outl…