The SCCRC listed no fewer than six grounds for serious concern about al-Megrahi's conviction, including the fact that the US Justice Department made an undisclosed payment of $3 million to two Maltese citizens whose evidence had linked al-Megrahi with the suitcase that contained the bomb. If the appeal had gone ahead, al-Megrahi's conviction would probably have been quashed.
That would have been deeply embarrassing for the Scottish authorities, especially since the evidence suggested there had been a deliberate attempt to frame the Libyan. But they did have the power to delay the hearing of his appeal for a very long time, and al-Megrahi was not a well man. So one can imagine a bargain being struck: his freedom for his silence.
Al-Megrahi never stopped protesting his innocence, but he did withdraw his appeal, so the new evidence was never heard in court, his conviction was never cancelled, and nobody was embarrassed. But why did the intelligence agencies pick on him in the first place?
Because they had to abandon their first working hypothesis, which was that flight 103 was destroyed in late 1988 as tit-for-tat Iranian revenge for the accidental shooting down of an Iran Air plane with 290 people aboard by the US warship Vincennes earlier that year.
But the investigation moved slowly, and 20 months after Pan Am 103 went down, Saddam Hussein's Iraq invaded Kuwait. The US was mobilising a coalition of Western and Arab armies to liberate Kuwait, and it wanted Syria to be part of it. But Syria was Iran's closest ally in the Arab world, so this was not the right time to get into a confrontation with Iran.
Nevertheless, somebody had to be punished or the intelligence services would look incompetent. The people who carried out the bombing for Iran had made some rudimentary attempts to put the blame on Libya, and the security services now started using that evidence to frame Megrahi. The evidence was full of holes but he was convicted anyway.
But with the appeal that would have exposed the truth smothered, all this remained mere conjecture until last week, when the al-Jazeera network broadcast an interview with Abolghassem Mesbahi, a former Iranian intelligence officer. Mesbahi, who once reported directly to the Iranian president, said it quite plainly: Iran's supreme leader, Ayatollah Khomeini, gave direct orders for the destruction of an American airliner after the Vincennes incident in 1988.
So the original hypothesis was correct, and the Western security services probably always knew it was correct. They don't care; the case is closed, and with Megrahi's appeal cancelled it will never be reopened.
But it is worth noting that he was an innocent man, not a mass murderer, and that his life was cynically destroyed by the same people who brought us the invasion of Iraq, mass surveillance, and so much more.
• Gwynne Dyer is an independent journalist whose articles are published in 45 countries.