Convicted Lockerbie bomber Abdel Basset al-Megrahi (L) talks with Libyan leader Muammar Gaddafi in Tripoli in this August 21, 2009 video grab from Libya TV. Gaddafi hugged the convicted Lockerbie bomber and promised more cooperation with Britain in gratitude for his release, while London and Washington condemned his "hero’s welcome" home. Meeting Megrahi and his family late on Friday, Gaddafi thanked British Prime Minister Gordon Brown and Queen Elizabeth for "encouraging" Scotland to release the dying prisoner from a Scottish jail, Libyan news agency JANA reported.
Abdelbaset Ali al-Megrahi has left Scotland to return to Libya.
With his departure, a lengthy chapter in Scots legal history has closed.
But many questions remain – and they will not disappear along with the flight to Tripoli.
BBC Scotlandâ€™s Home Affairs Correspondent Reevel Alderson has been looking at the mystery which still surrounds the 1988 bombing.
The collection of evidence from Britainâ€™s worst act of terrorism began immediately – and within a week detectives announced it had been caused by a bomb in a radio cassette player.
Throughout the subsequent weeks whole sections of the jumbo jet were recovered to help investigators literally piece together the cause.
Although they knew it was a bomb they needed to find out who had placed it, why they had done so, and how?
Early suspicion fell on Ahmed Jibril, leader of Palestinian terror group the PFLP-GC, who intelligence sources suggested may have been working for Iran.
West German police mounted Operation Autumn Leaves, raiding flats near Frankfurt where the group was preparing bombs in radio cassette players.
They were similar to that used to blow up Pan Am flight 103.
But Dick Marquise, chief of the FBI â€œScotbom Task Forceâ€ from 1988-1992, said investigators could find nothing later to link this plot with Lockerbie.
â€œWe never found any evidence,â€ he told the BBC. â€œThereâ€™s a lot of information, thereâ€™s a lot of intelligence that people have said there were meetings, there were discussions.
â€œBut not one shred of evidence that a prosecutor could take into court to convict either an official in Iran or Ahmed Jibril for blowing up Pan Am flight 103.â€
There were also suggestions that Jibrilâ€™s group put the bomb onto a Pan Am feeder flight from Frankfurt Airport to Heathrow, switching the suitcase for one containing drugs being run by another Palestinian group.
But another airport has also come under suspicion – Heathrow in London, from where the doomed jumbo jet took off.
Dr Jim Swire, whose daughter Flora was one of the victims of the atrocity, said a break-in the night before near the Pan Am secure baggage area was not fully investigated by police, who he claims concealed the evidence.
â€œI wrote recently to the Crown Office (which handles Scottish prosecutions) asking why that had been concealed for 12 years, and if they knew about it all along,â€ he said.
He said they would not answer his question, which he said meant there must now be a thorough inquiry into the incident.
During Megrahiâ€™s first appeal, held at Kamp van Zeist in the Netherlands, his counsel raised the matter, saying it cast doubt on claims that the fatal bomb must have been loaded in Malta.
But the five appeal judges rejected the suggestion.
Malta had become crucial once police found a fragment of the bomb timer wrapped in a piece of clothing in a Dumfriesshire forest.
The clothes had Maltese labels – but question marks remain about how this discovery was made several months after the disaster, and also over how the material was handled.
The original trial heard labels on police evidence bags containing the fragment had been changed: the evidence of the officer who had done this was heavily criticised by the trial judges.
There were question marks too over Tony Gauci, a Maltese shopkeeper who was the only man to identify Megrahi.
His evidence was that the Libyan, who he picked out at an identity parade, had bought the clothes at his shop.
But his police statements are inconsistent, and prosecutors failed to tell the defence that shortly before he attended an identity parade, Mr Gauci had seen a magazine article showing a picture of Megrahi, and speculating he might have been involved.
Mr Gauci now lives in Australia, and according to defence claims is believed to have been paid several million dollars by the Americans for his evidence.
It may be that we will never know exactly what happened in December 1988.
Secret documents before the Appeal Court – which even the defence has not seen – might have provided new information.
They will now remain undisclosed, after the foreign secretary issued a Public Information Immunity certificate stating that to publish them would be to the detriment of UK national security.
Megrahi was charged as a member of the Libyan Intelligence Services – acting with others.
Megrahi is now dying, but he may have been a convenient scapegoat for a much bigger conspiracy.