The Harvard law professor Alan Dershowitz has argued that for just this reason, a president cannot be guilty of obstruction. Mr. Dershowitz notes, moreover, that the Constitution gives the president pardon power. President George H. W. Bush thwarted the Iran-contra investigation by pardoning former Defense Secretary Caspar Weinberger, and President Gerald Ford shut down the investigation of Nixon by pardoning him. Mr. Trump could easily end the Flynn investigation with a pardon, Mr. Dershowitz reasons, so he could also shut it down with a request to the F.B.I. chief.

But Mr. Dershowitz is wrong. The president’s law enforcement discretion is not unlimited. He can’t, for example, order prosecutors to enforce drug laws against black people but not white people. He also can’t drop an investigation in exchange for a bribe. He can stop an inquiry for a wide range of reasons but not for “corrupt” purposes. The same is true with respect to pardons: While the president most certainly has this power, we know of no one who believes that the president can simply sell pardons for cash.

Mr. Mueller must now decide where to draw the line between “corrupt” intent and the legitimate exercise of prosecutorial discretion. He might start by looking at the Justice Department’s own regulations, which prohibit prosecutors from taking part in an investigation in which they have a “personal or political relationship” with the subject. Under that standard, Mr. Trump’s involvement in the Flynn investigation is immediately suspect. If Mr. Trump intervened to save a close associate and political ally from indictment, then the argument that he acted “corruptly” would be strong.

The president’s constitutional responsibilities do make his standard of conduct more nuanced than that of an ordinary prosecutor. If Mr. Trump tried to block the investigation of Mr. Flynn because he believed that the inquiry would bring us to the brink of war with Russia, then that would suggest a noncorrupt intent. Mr. Mueller will have to ask not just what the president did but also why he did it.

By carefully considering this question, Mr. Mueller would be fulfilling his mandate, which extends to obstruction allegations arising out of his initial investigation. And even if he decides not to charge the president, his findings may show that Mr. Trump has abused his power in ways that would warrant impeachment, if not indictment.

Yet it is possible that Mr. Mueller will himself be thwarted before he reaches the end of his inquiry. Mr. Trump has reportedly considered firing the special counsel. If he does, the president will have interfered not only with the investigation of his campaign’s Russia ties but also with the investigation into his own possible obstruction of the investigation. Covering up a cover-up would be yet another crime. In this, as in so many ways, Mr. Trump would break new ground.