In 2013, hundreds of CIA officers — many working nonstop for weeks — scrambled to contain a disaster of global proportions: a compromise of the agency’s internet-based covert communications system used to interact with its informants in dark corners around the world. Teams of CIA experts worked feverishly to take down and reconfigure the websites secretly used for these communications; others managed operations to quickly spirit assets to safety and oversaw other forms of triage. “When this was going on, it was all that mattered,” said one former intelligence community official. The situation was “catastrophic,” said another former senior intelligence...