They lied, they're still lying, and they'll go on lying until Libya calms down enough to allow a thorough search of its archives. That's what intelligence agencies do, and being angry at them for lying is like being angry at a scorpion for stinging. But we now know that they
The framing of innocent man
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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 long time and al-Megrahi was not a well man. So one can imagine a bargain being struck: his freedom for his silence.
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 Pan Am 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 that year.
Since the Iranians didn't have people in the right places with the right skills to do this job, US intelligence believed, it paid Palestinian terrorists to do it. The US even fingered the Popular Front for the Liberation of Palestine - General Command, as those who took the contract.
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 wanted Syria in. 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 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 the Libyan's defence team did a poor job of exposing them and he was convicted anyway.
The reason his defence team did so badly may have been that the Libyan dictator, Muammar Gaddafi, had made a deal: to be released from a crippling trade embargo, he would admit the blame for the Pan Am bombing and pay compensation to the families of the victims. For that deal to stand, Megrahi had to go down. A few threats to his family back in Libya would have persuaded him to sabotage his own defence.
But with the appeal that would have exposed the truth smothered, all this remained mere conjecture until this month, 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 plainly: Iran's supreme leader, Ayatollah Khomeini, gave direct orders for the destruction of a US airliner after the Vincennes incident in 1988.
So the original hypothesis was correct, and the Western security services probably always knew it. They don't care; the case is closed, and with Megrahi's appeal cancelled it will never be re-opened. 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 more.