While the strong resistance to Mr. Trump within the executive branch — and the rather weak pushback from outside — may defy traditional notions of separated powers, it is not hard to explain.

First, the aides who bucked the president’s efforts to interfere with the Mueller investigation had political and professional fates separate from Mr. Trump’s. For example, Mr. McGahn, a former member of the Federal Election Commission, had a lucrative partnership at the law firm of Jones Day to which he could return after his Trump administration stint — provided that he did not so sully his reputation while White House counsel that he would scare away clients or get himself disbarred.

Second, in several cases the specter of legal liability appeared to play a role. Mr. McGahn and Mr. Priebus often consulted their shared personal attorney when deciding to defy their boss. The shadow cast by the special counsel’s inquiry thereby contributed to defiance from within the White House, while this defiance also shielded the special counsel from presidential interference. For lawyers in the administration — including officials like Mr. Priebus who did not occupy a legal post but planned to return to law practice afterward — professional norms exerted an additional constraint. Disbarment for an attorney is career death.

Nor does the pardon power turn out to provide the president with carte blanche over the executive branch. The people before whom Mr. Trump dangled the possibility of a pardon could not be sure that the volatile president would follow through. A pardon, moreover, does not repair damages to one’s reputation.

Can the president evade these limitations by filling key posts with cronies? Not really. Filling posts with individuals whose only qualification is their loyalty produces less pushback but more bumbling. So far, Mr. Trump has oscillated between reliance on competent aides who have resisted his instructions and on yes men who have fumbled his orders.

In his great essay, Federalist Paper No. 48, James Madison famously warned that the mere “parchment barriers” of the Constitution could not prevent a descent into tyranny. What is mostly forgotten is that he feared the legislature more than the executive. As to the executive power, he said, “being more simple in its nature,” “projects of usurpation” would “immediately betray and defeat themselves.”

Whether or not that is true in every case, it was certainly so with Mr. Trump. By trying to obstruct an investigation that had the potential to embarrass his administration, he ensured only that the investigation would expand to encompass his desperate measures to stop it, bringing to light further evidence of the incompetence and moral rot of his leadership. These developments will make the president’s subordinates even less willing than ever to take a bullet for their boss.