These are not happy times at the F.B.I. Morale at the country’s premier law enforcement agency plummeted months ago, after James B. Comey, its director, revived the investigation into Hillary Clinton’s use of a private email server in October and plunged the bureau back into the political maelstrom just before the election. Then President Trump fired Mr. Comey on Tuesday, saying he had mishandled the Clinton investigation, and the mood darkened again. Agents said they were stunned that Mr. Trump would fire Mr. Comey in the midst of an F.B.I. investigation into whether any of the president’s associates had conspired...