In hopes of protecting future prosecutors from Mr. Cox’s fate, Congress created the independent counsel in 1978, an officer who would be more autonomous. If an attorney general determined there were credible allegations against a president or other high officer to be investigated, an independent counsel was selected by a three-judge panel. Such a prosecutor had more latitude, was obliged by law to report possible impeachable offenses by the president to Congress and could be fired by the attorney general only for “good cause” or disability.
Neither party ended up being all that happy with the independent counsel structure, becoming convinced it was a blank check that led to endless investigations. Republicans were soured by Lawrence Walsh, the independent counsel who investigated President Ronald Reagan and the Iran-contra affair, while Democrats grew disenchanted by Ken Starr, whose Whitewater investigation morphed into the impeachment of President Bill Clinton for lying under oath about an affair with a former White House intern.
By the end of Mr. Clinton’s administration, there were seven independent counsels investigating him or his top officials, and the law was allowed to lapse in 1999. Instead, the Justice Department created a regulation for the appointment of special counsels who would answer to the attorney general and therefore be less likely to wander too far afield.
But the experience of Robert S. Mueller III, the special counsel who investigated Mr. Trump’s campaign for ties to Russia, underscored for many the weakness of this structure as well. Since a special counsel reports only to the attorney general, it still falls to a president’s appointee to decide any legal action.
Because of a longstanding Justice Department opinion that a president cannot be prosecuted while in office — a judgment crafted under two presidents who faced allegations, Nixon and Mr. Clinton, and never tested in court — Mr. Mueller opted not to say whether he thought Mr. Trump had committed obstruction of justice even though his final report included evidence that the president had.
Moreover, the results of a special counsel investigation are not required to be released to the public nor even submitted to Congress. In the Russia case, Attorney General William P. Barr agreed to make public a redacted version of Mr. Mueller’s report, but only after framing its contents in terms favorable to Mr. Trump and declaring that there was no obstruction case, moves that drew howls of protest from Democrats.
If there has yet to be a structure, then, that has won wide acceptance as a rational and independent way to investigate a president or other important figure, the Mueller case demonstrated how hard it will be to ever separate politics from prosecutions. Even Mr. Mueller, a former F.B.I. director and lifelong Republican with an impeccable reputation as a straight shooter, saw his reputation marred by the relentless attacks from Mr. Trump and his partisans.