Some of us who questioned the conduct of the Scottish Government leading up to and following the trial of Alex Salmond nevertheless recoiled at suggestions that a grand conspiracy was afoot. Occasionally to question the competence and even the sincerity of your ministers of state is a primary function of a free press in any progressive democracy. To accuse your government though, of a conspiracy which nudged the borders of outright criminality is the stuff of a fevered imagination, isn’t it?

And not just any old conspiracy. This one would have condemned your country’s greatest political leader to a prison cell. It’s surely stretching credibility to suggest that a star chamber of current and former ministers, led by your serving Premier and aided by senior advisors and civil servants would have even attempted to carry out such a chilling plot. Isn’t it?

Even as the unanswered questions and evasions began to emerge we still held fast to the position that they had all been the result of political over-reach: still a serious matter of course, but something that happens in even the most civilised and mature of democracies. Or that the investigation into Mr Salmond had been so widespread and had involved taking statements from so many potential witnesses that of course recollections could become hazy. Or that the two-year period which covered these events involved senior figures from every realm of the state: judicial, legislative and political, meaning that a complex web of overlapping interests - almost unprecedented - had to be navigated. The public would surely understand any honest mistakes. Wouldn’t they?

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And that’s assuming that many of them possessed a detailed understanding of how all these moving parts were supposed to work anyway. Best that they don’t bother their pretty little heads with the minutiae and trust - as always - that, no matter what, they were always acting within the law and in their best interests and in the interests of justice. And if some doubts still remained, why we could count on some of our courtiers to sing them lullabies about Nicola and her friends: go to sleep; nothing to see here: all is calm; all is bright.

But the questions wouldn’t go away. Who leaked details of the complaints to a tabloid, endangering the right of the complainers to have complete anonymity? Why was the initial investigation so incompetently conducted and so tinged by apparent bias that it cost the public £500k to settle it? And why was no-one held to account for this?

Why was the Scottish Government so desperate not to release evidence to the Hamilton Inquiry into whether or not Nicola Sturgeon had misled the Scottish Parliament over the Alex Salmond affair? Surely there was nothing to hide. James Hamilton had already concluded that Ms Sturgeon, forgetful though she may have been, had not breached the ministerial code. Indeed, the Scottish Government had treated the Scottish Information Commissioner with abject contempt in delaying the release of the data until the last possible minute. In doing so, it was also treating the public with contempt. Effectively, Scottish ministers were saying: “we don’t think this is very important and you the public shouldn’t be bothering about stuff that’s miles above your heads and doesn’t concern you.”

Of course, we expected the redactions in the evidence when it finally arrived. Yet there was still plenty in it pointing to a troubling operation at the heart of all of this. It may not yet have reached the level of "conspiracy" but that still leaves room for "cover-up" and "distortion".

We know now that Scottish ministers provided the Information Commissioner with misleading information. We know too that there was not sufficient distance between ministers and the Hamilton Inquiry. Effectively, this meant that its independence was undermined from the outset by the presence and actions of an unnamed senior civil servant who was advising both the Government and the inquiry. We know now that this individual was part of the secretariat, a detachment of civil servants tasked with working on the Hamilton Inquiry.

Joanna Cherry, a senior KC, was concise in her immediate observations. “First, Scottish ministers made misleading statements to the information commissioner. Second, the appeal proceeded in the face of advice from counsel that the prospects of success were weak. And third, the frequent redactions of the name of a civil servant whose actions appear to be central to the whole saga.”

James Hamilton ruled that Nicola Sturgeon had not breached the Ministerial CodeJames Hamilton ruled that Nicola Sturgeon had not breached the Ministerial Code (Image: PA)

There are still currently several ongoing investigations into the handling of the Alex Salmond case, including a criminal one. And so, care must be taken about reaching any hard and fast conclusions in the meantime. However, one huge aspect of it has become clear in the Scottish Government’s conduct throughout all of it. It speaks to something rotten at the heart of this administration that travels well beyond the Salmond affair.

The accepted wisdom about why this Government has sought at every step of the way to thwart attempts to get at the truth is that it might prove embarrassing and undermine whatever legacy Nicola Sturgeon and her cohort are hoping to leave. But the delay in producing evidence of its workings and its evasions was in the hope that the public will have long forgotten what it was all about in the first place. And that, in the course of leading real lives with problems in real time the public will view much of this as the political elites counting angels dancing on a pin. These people know that the public grants them significant leeway in how they conduct themselves: that there are affairs of state best left to them and that - so long as they don’t take liberties and don’t get caught with their hands actually in the till - we’ll let them get on with it.

But there are serious questions surrounding the Salmond affair that ought to chill us. To what extent has a small government within a government been allowed to suborn those institutions that stand as bulwarks of a state’s claims to be civilised?

If our government can commit many thousands of pounds defending the indefensible while deliberately undermining institutions and offices of state we consider to be sacrosanct and think the normal rules of decency and honesty don’t apply to them, then Scotland is in a dark place indeed.

If they can do that, how easy will it be for them to come after those who have neither the money, the knowledge nor the connections to defend themselves?

Kevin McKenna is a Herald writer and columnist. This year is his 40th in newspapers. Among his paltry list of professional achievements is that he’s never been approached by any political party or lobbying firm to be on their payroll.