The Justice Department
Closely related to the first obstacle is the need for any such prosecution to receive the sign-off of the Justice Department, which, though staffed by political appointees in its upper echelons, is primarily comprised of career government lawyers.
Thus, career lawyers played an important voice in recommending against the prosecution of former Bush administration officials for their role in the torture of terrorism suspects early in President Barack Obama’s tenure, and similar opposition might also arise from efforts by the new attorney general to pursue a prosecution.
There is also important historical precedent for even political appointees in the Justice Department to stand up to the President — most notably the “Saturday Night Massacre,” when the attorney general and his deputy both resigned rather than comply with President Richard Nixon’s order that they fire the special prosecutor investigating Watergate.
On the trail, Trump has also called for appointment a special prosecutor — which might allow him to sidestep the career lawyers in the Justice Department’s Criminal Division. But such a maneuver is usually reserved for cases in which the Justice Department would have a conflict of interest (including, for example, investigations of current Executive Branch officials as with what happened with President Bill Clinton), which does not seem to be at issue here.
The Grand Jury
Even if the Justice Department signs off on a prosecution under these circumstances, the Constitution creates a series of significant structural checks on the Executive Branch in such cases, the first of which is the Fifth Amendment’s requirement of a grand jury indictment for serious offenses — such as those Secretary Clinton has been accused of committing.
Under federal court rules, the grand jury is comprised of somewhere between 16 and 23 citizens from the district in which the case is being brought (which would likely have to be either the District of Columbia or the Southern District of New York) — 12 of whom must vote in favor of an indictment for the case to go forward.
Of course, the standard the prosecution must meet is relatively modest — demonstrating only that there is “probable cause” to believe that the accused is guilty of the charged offense. But even then, the grand jury serves as an important check on potentially overzealous (or politically motivated) prosecutions. Thus, even if Trump were to overrule the objections of the FBI and the Justice Department, he could not force a grand jury to return an indictment.
The Trial Court
The last legal obstacles to such a prosecution would come from the trial court — from an independent, life-tenured federal judge who could dismiss any indictment that he found to be legally insufficient, and from a jury of 12 of Clinton’s peers, which would have to be unanimous in its belief that she was guilty beyond a reasonable doubt to convict her of a crime.
Although it is all but impossible to fathom a prosecution getting even this far because of the obstacles discussed above, these last two checks are perhaps the most significant — and the reason why even the most politically motivated government prosecutors would almost certainly balk before bringing such a case. Indeed, federal district judges may have no more important single function than ensuring that criminal cases are brought only when there is sufficient evidence to sustain an indictment — and the guarantee of criminal trial by jury has long been viewed as one of the most fundamental of all of the Constitution’s protections of individual rights.
But whereas the above considerations go to the legal and bureaucratic obstacles to a prosecution of Clinton arising out of her use of a private e-mail server to conduct official State Department business, and why she could not be prosecuted, perhaps the most significant and fundamental reason why a President Trump should not — and would not — pursue such a case is because of the ugly precedent it would set.
Thanks to the obstacles identified above, any such prosecution would be transparently political, and would thereby set a precedent pursuant to which newly elected presidents might seek to pursue trumped-up charges as a way of silencing their opponents — or use the specter of such prosecutions as a means of intimidating those who would run against them.
But as then-Attorney General (and future Supreme Court Justice) Robert Jackson warned in a celebrated 1940 address, “It is in this realm — in which the prosecutor picks some person whom he dislikes or desires to embarrass, or selects some group of unpopular persons and then looks for an offense, that the greatest danger of abuse of prosecuting power lies. It is here that law enforcement becomes personal, and the real crime becomes that of being unpopular with the predominant or governing group, being attached to the wrong political views, or being personally obnoxious to or in the way of the prosecutor himself.”
And abuses of prosecutorial power, Jackson warned, not only demean the integrity of the entire criminal justice system, but, even worse, they can beget further abuses — by future Presidents — against the very prosecutors who started the vicious cycle.
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