Robert Mueller has a reputation as a straight-shooting, play-it-by-the-book sort of guy. That changed this week. The special counsel’s stated justifications for not accusing Donald Trump of obstruction of justice appear convoluted and legally dubious. Mueller was a man hired to solve a mystery. His odd decision to take refuge in questionable precedents, and thereby effectively duck the issue, has only compounded it.

His two-year investigation was admirable in many ways. Unlike similar exercises in the past, such as Kenneth Starr’s 1990s inquiry into Bill Clinton, he kept his counsel, did not leak to the media, and completed the business within a reasonable timeframe. His finding that there were “multiple, systematic” Russian efforts to interfere in the 2016 presidential election is clear and unambiguous.

But when it comes to Trump, Mueller wobbles. His usually precise language becomes tortuous, even labyrinthine. “If we had confidence that the president clearly did not commit a crime, we would have said that. We did not, however, make a determination as to whether the president did commit a crime,” Mueller declared from atop the US Department of Justice podium.

What did he actually mean? That he has no confidence in Trump’s innocence? That he suspects the president is guilty as hell, but is unable to substantiate the charge? Or that he simply does not know either way? By way of explanation, Mueller went on to say that Department of Justice past practice prevented him from bringing an indictment and, in any case, to do so would be “unfair”.

On the basis of evidence detailed in Mueller’s own report, there is every reason to believe Trump attempted to obstruct justice on multiple occasions. As a former federal prosecutor and head of the FBI, Mueller knows what it takes to make a case. The report cites 10 instances of blatant obstruction. The ammo is there. So the real question – the real mystery – is: why did Mueller not take the shot?

In case the report’s damning findings have been obscured by White House spin and the ensuing political bunfight, it is worth recalling just how persistent were Trump’s attempts to thwart the inquiry. In one instance, Mueller found, Trump leaned on James Comey, the then FBI chief, to let off Michael Flynn, his national security adviser whose lies about his Russian contacts led to his sacking. “Now that we fired Flynn, the Russia thing is over,” Trump told an adviser. Wrong.

As Mueller has unsatisfactorily left it, Trump is above the law, yet not above suspicion

In other instances of obstruction cited by the report, Trump sacked Comey in the apparent hope it would keep the Russia investigation away from him personally; demanded, in a panic, that Mueller be dismissed and later denied he had done so; attempted to force Jeff Sessions, the then attorney general, to intervene publicly to undermine confidence in the impartiality of the investigation; and tried to prevent or manipulate disclosure of evidence by the media.

If all this does not amount to a persuasive prima facie case for obstruction of justice, it is extremely difficult to see what would. There can be little doubt that if anyone other than the president were involved, criminal charges would have been filed – as has been the case with several campaign associates. For as the constitution defines them, these are impeachable “high crimes and misdemeanors”.

In short, Mueller had Trump bang to rights – so surely his arguments for not proceeding must be powerful indeed? Not so. Legal experts and law professors have been popping up ever since Mueller spoke, pointing out that the Department of Justice’s settled “opinion” that a president cannot be prosecuted while in office has never been tested in court. There is no legal bar to Trump’s indictment.

Similarly, Mueller’s secondary argument that to indict Trump would contravene the “principles of fairness” assumes the president would be unable to clear his name in a court hearing – when in fact, it might be fairer, to him and the American public, to afford him that opportunity by bringing charges. As Mueller has unsatisfactorily left it, Trump is above the law, yet not above suspicion. Not guilty, but not exonerated, either.

The underlying mystery is why Mueller did not accept the evidence of his own eyes, and his own inquiry, and formally set out the grounds for an indictment, even if he believed it could not be immediately pursued. “The fact that a president cannot be prosecuted does not foreclose a finding by a special counsel of whether a president committed a crime,” J Michael Luttig, a former federal judge, told the Washington Post.

Even William Barr, Trump’s attorney general and apologist-in-chief, reportedly expressed surprise that Mueller had not made a definitive determination over the obstruction allegations. Barr quickly and effectively exploited the omission. He declared it meant Trump had no case to answer – which could not be further from the truth.

Perhaps in the end, Mueller, a lifelong Republican, did not want the blame for taking down a Republican president. Perhaps his privileged East Coast upbringing and gilded career inside the old Washington establishment rendered him unsuited to the modern-day role of king-slayer. Perhaps he believes, as a matter of principle, that Congress, not the courts, is the proper place to dethrone a president.

But there is another, grimmer possibility. Trump has spent much of the past two years doing his noisy, bullying best, in public and in private, to undermine, discredit and pressure what he called the special counsel’s Russia “witch hunt”. Like others before him, was Mueller ultimately influenced in some way by this relentless, ruthless campaign of intimidation? After all, it’s how Trump wins. And it’s how the US loses.

• Simon Tisdall is a foreign affairs commentator