AP Photo

Just after noon on Dec. 29, Julie Hughes, the Egypt country director of the U.S.-based National Democratic Institute (NDI), got a phone call saying police were raiding the group’s office in the south. Thirty seconds later, over a dozen men, roughly half of them armed with AK-47s, burst into her Cairo headquarters, while other teams assaulted the NDI’s offices in Assiut and Alexandria. “It was impressive logistically,” Hughes recalls. As the officers piled in, she immediately called the NDI’s local lawyer, then the American Embassy. A man in dark glasses commanded her to hang up. Hughes told him she was an American citizen. “Hang up the phone or we’ll take that too,” he snapped. They wouldn’t tell her who ordered the raid, only that they called him “Mr....