President Trump had barely returned to power last year when Hector F. Ruiz, a veteran civil rights lawyer for the Justice Department, shared a directive with his team that some found chilling. He told the team that he had been instructed to open investigations into more than a dozen universities, according to two people with direct knowledge of the meeting. The orders were a sharp break from the department’s norm of collecting facts before proceeding with a formal inquiry, and some investigators viewed the demand as a politically motivated attack. Within months, Mr. Ruiz and 17 of his team’s lawyers...