William McGovern was a prosecutor out of central casting, a tough, careful fellow who has tried murderers and money launderers during a distinguished career in New Jersey.

So he seemed a natural man to turn to in 2010 when the Hunterdon County prosecutor needed to investigate a politically sensitive case centering on the county’s Republican sheriff and two deputies who had connections to the new Republican governor, Chris Christie. Mr. McGovern, who is a Republican, led the investigation, took the case to a grand jury and emerged with a 43-count indictment, alleging abuses of power.

On the day the indictment was unsealed, the New Jersey attorney general seized control of the Hunterdon prosecutor’s office and soon took the highly unusual step of quashing those nettlesome indictments. That shook the entire office; another prosecutor, Bennett Barlyn, complained that the decision was corrupt, and security guards escorted him out of the office. Within weeks, he was fired.

Not long after, Dermot O’Grady, the deputy attorney general put in charge of Hunterdon, called Mr. McGovern into his office. He advised him: Stay quiet. He told the prosecutor it “wouldn’t be in his best interests” to talk about this case, according to a memo that Mr. McGovern wrote to himself that same day.