The knee-jerk response to yesterday’s decision to refer the case of the Lockerbie bomber to Scotland’s High Court of Justiciary will be straightforward and brutal: this was a body-blow to a judicial system that has always prided itself on the highest standards of integrity and rectitude.

Scots Law is fundamentally different from English; it derives from the continental system of Roman Law, and has certain checks and balances that protect the innocent from miscarriages of justice; it is, as the great judicial expert Lord Stair once said, “the dictate of reason”.

Therefore, when the Scottish Criminal Cases Review Commission announced that it believed that the Libyan bomber might, after all, have been wrongly convicted, it appeared to set at nought 13 years of investigation on which the whole weight of the Scottish political and legal establishment, its combined police forces, and the intense behind-the-scenes diplomacy that brought two Libyan suspects to a specially constituted court in the Netherlands, had been brought to bear.

How could a simple confusion over dates have been overlooked by a defence team that had spent years combing through mountains of evidence, and by three of the most senior judges in the land? How could a man be convicted of the worst terrorist outrage in postwar Britain when, it now emerges, the circumstantial evidence against him was flawed, and he might never have been in the Maltese shop that was central to the prosecution case? That five Scottish Secretaries, three First Ministers, six Lords Advocate, and an entire panoply of judges and QCs presided over what may now turn out to be a spectacular miscarriage of justice, is surely a condemnation of the entire system.

To which the response is: not necessarily. There is a strong case to say that, on the contrary, the wheels of justice may have ground exceedingly slow, but in the end they seem to have come to rest in the right place. If, when Al-Megrahi’s appeal is finally heard, he is freed, then justice will finally have been done. At the same time, the ranks of the conspiracy theorists, who have been pouring out stories that range from the fantastical to the downright unbelievable, almost since Pan Am 103 was blown up over Lockerbie, have been sent packing.

What emerges from the Commission’s summary of its conclusions (which themselves amount to some 800 pages of closely argued evidence) is that the wilder claims about planted evidence and manipulated facts were unfounded; that the mysterious detective who has been spreading stories about CIA involvement was an unreliable witness; and that allegations that scientific material had been maliciously doctored, were simply untrue. Now, it is still possible that, at the appeal case, new evidence will be produced to reinstate these claims. But for now they have been knocked out of court. No one can accuse the Commission – which draws its membership from lay members as well as criminal experts, and has had three years to comb through all the allegations – of being an Establishment poodle.

We can, therefore, conclude that the police investigation was professionally carried out; the evidence was dutifully assembled; the trail that led from the scattered wreckage around Lockerbie to a clothes shop in Malta was well established; the Libyan connection seemed, on the surface, convincing.

What is damning, however, is the way that new evidence that casts doubt on Al-Megrahi’s involvement was never properly challenged, and that certain material, available to the prosecution, was never shown to the defence team. Withholding such evidence is a basic breach of court procedure, and there will be serious questions asked at the appeal stage about why it happened. All is not well with a system that can overlook such a fundamental process, and the Commission was right to say that it calls into question the safety of the conviction.

What it does not do, however, is blow an entire legal system out of the water.

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