Some 38 minutes after Pan-Am Flight 103 Maid of the Seas left Heathrow en route to New York, a bomb built into a Toshiba radio-cassette player, placed inside a Samsonite suitcase, went off.

The brief horror inside the aircraft's cabin and flight deck is unimaginable. All on board the disintegrating jet were killed – 243 passengers and 16 crew – and 11 people died on the ground in Lockerbie. It remains the deadliest single terror attack on European soil.

In the fantasy world of Hollywood CSI science, Lockerbie would be a closed case. Meticulous factual analysis would be unchallengeable. Justice would be seen to be done. Reputations would be forged by its success. Feature films would celebrate dogged heroes determined to find the truth. The reality? Despite a mountain of evidence and a supposedly ground-breaking Scottish trial on "neutral" territory in the Netherlands before learned judges, Lockerbie remains a byword for state silence on evidential inconsistencies, surrounded by dark, covert diplomatic games.

A Libyan, Abdelbaset al-Megrahi, was convicted of mass murder in 2001 and sentenced to 27 years in jail. In 2009, supposedly on compassionate grounds, he returned home to die of prostate cancer, which he did in 2012. He remains the official answer to the question: who did this? However, the evidence against Megrahi now wouldn't stand up in any court – unless that court were one where verdicts are determined ahead of what's heard, and any duty to disclose evidence which doesn't suit the prosecuting authorities is seen as an unnecessary luxury.

Lockerbie, then, is a stain on the Scottish legal system; dirty judicial laundry that Alex Salmond and his nationalist administration would rather remained bagged up until well after next year's independence vote. This is one reputation which, if tarnished, would have immediate political implications.

In the months after the mid-air explosion, debris was recovered from hundreds of square miles of Scottish and Northumberland countryside. Pieces from an aluminium cargo hold container – marked AVE4041PA – were pieced back together. Official evidence by the Air Accidents Investigation Branch identified this container as the location of the blast.

For the Semtex hidden inside the radio to have had the effect it did, breaking through the fuselage and creating a small hole that led to the "skin" of the aircraft peeling off at 31,000ft, the suitcase must have occupied a precise bottom-row location inside AVE4041, close to the edge of the plane's hull.

Seven aluminium containers had been filled with the luggage of Pan-Am passengers who had checked in at Heathrow's Terminal 3. The eighth container, AVE4041, was for baggage from a transfer flight from Frankfurt. No security screening of the Frankfurt luggage took place. It was assumed that this had been done in Germany. The feeder flight was due at 17.20. Pan-Am 103 was timed to push off at 18.00.

One of the staff in the loading area where AVE4041 was being filled was John Bedford. He told police in a statement given in January 1989 that he noticed a hard-shell Samonsite suitcase had already been loaded into the bottom of the "tin" container before the feeder flight had even landed.

If an inquiry is ever allowed to re-examine the Heathrow luggage procedures, security in the baggage area at Terminal 3 and the timing and chances of a bag from a late-arriving feeder flight being accidentally placed exactly where needed to blow a hole in a 747's fuselage, the currently accepted account will be made to look ridiculous. Adequately Explained by Stupidity, a new book by Dr Morag Kerr, from the Justice for Megrahi (JFM) team, focuses largely on Heathrow.

Bedford's account has altered over time, but what he said first remains crucial. If correct, what happened before Heathrow – in Frankfurt and Malta, where Megrahi was supposed to have placed the unaccompanied suitcase bomb on flight KM108 from Luqa, which later transferred to Pan-Am 103 – is all irrelevant.

Take Malta out of the equation, and Libya's alleged role in the bombing fades dramatically. But how did Libya figure in the first place? If Flight 103 had been delayed, which is common enough at busy Heathrow, the bomb, if on a simple timer set in Malta, could have exploded with the plane yet to take off. A small hole at ground level would have killed no one. But if the device used was barometric, triggered by atmospheric pressure levels, why did it not detonate on the Luqa-Frankfurt-Heathrow flights?

Terrorist groups in the frame in the early weeks and months of Lockerbie had links to the Palestinians, Syrians, Jordanians and Iranians. Libya would have been in the mix. The motives were varied – anything from state-sponsored revenge against the US, to murkier aspects of covert bilateral deals that backfired. The initial suspects were from the Popular Front for the Liberation of Palestine General Command (PLFP-GC), a Syrian-based terror group headed by Ahmed Jibril. A Maltese chapter of the group was on international intelligence radar. Frankfurt, as the location where the bomb was apparently loaded, had not been discounted.

Another early suspect was Mohammed Abu Talb, an Egyptian member of the Palestinian Popular Struggle Front (PPSF). When Talb was arrested in Sweden on suspicion of being involved in the bombing of a train in Denmark, items of clothing found at his house were traced to a Maltese manufacturer.

According to informed media reports in 1989, Talb had links to the PLFP-GC and had been in Malta with a known terrorist bomb expert. This information was regarded as sound enough for Scottish police to plan a trip to Sweden to interview Talb in prison. The case against him never progressed. However, a report by Megrahi's team in 2002 suggested that Talb was still in the frame at precisely the time that attention switched to Megrahi.

In January 1989, a scrap of shirt collar was found in the area of debris where most of AVE4041 was recovered, The singed material held fragments of the Toshiba radio casing, some speaker mesh and a fragment of a printed circuit board. That fingernail-sized bit of board was to gain prominence in the summer of 1990.

The Scottish police failed to source the origin of this evidence, labelled PT/35b. But a joint effort by the CIA and the FBI in June 1990 matched the circuit board to a timer held in a Langley archive that had been part of a coup attempt in Togo, West Africa. At any future inquiry, the FBI should be asked, why they visited the Zurich offices of Mebo, the timer company, a month before the Scottish police were told of the timer's ID.

The link to Libya was now advanced. It was claimed that the PT/35 fragment was part of an MST-13 timer unit – a specific Mebo order from the Libyan armed forces. By January the following year, Megrahi, a Tripoli airport control manager briefly assigned to Libyan intelligence for bureaucratic rather than specialist tradecraft reasons, was on the investigation's radar.

For a journalist who has observed 25 years of the changing importance of key Lockerbie evidence, examined allegations of deliberate non-disclosure, new whodunnit theories and material reinterpreted for the appeals launched by Megrahi's lawyers, there's an overwhelming sense of one thing – a lack of certainty. What is certain is that the Mebo fragment, a principal piece of evidence against Megrahi, holds none of the hallmarks claimed for it by the prosecution at the Camp Zeist trial in the Netherlands. Mebo gave the investigation control samples from the original batch that had been produced in an outsourced deal with a company called Thuring. Expert technical witnesses claimed that there was no material difference between the Thuring sample and the fragment recovered from the debris. That wasn't true.

During preparations for Megrahi's second appeal, tests showed that the PT/35 fragment was manufactured with a pure tin coating, and the Thuring sample was covered with a standard alloy of tin and lead. The pure tin manufacturing method had never been used by Thuring and all the circuit boards supplied to the Libyan armed forces involved the Thuring process. So whatever PT/35b was, it did not match the timers ordered by and supplied to Libya.

The Mebo-Libya link was crucial to Megrahi's conviction. This is still regarded as key evidence. But without the Malta flight connection and without the timer fragment's Libyan origins, the case against him falls apart. If these developments had been openly scrutinised in court at a second Megrahi appeal, the Scottish police and judiciary risked being made to look, at best, like a collection of amateur investigators.

Details of a second appeal in 2007 were examined by the Scottish Criminal Cases Review Commission (SCCRC). The commission's report granted leave for the Megrahi conviction to be challenged. Six grounds were cited as cause for serious concern, including undisclosed payments of around £2m by the US Justice department to Tony and Paul Gauci, the owners of a clothes shop in Sliema, near Malta's airport. Like the Samsonite case's journey from Luqa to Heathrow, and PT/35's link to Libya, the case against Megrahi required someone to link him to the suitcase. Tony Gauci provided the link.

Among the recovered debris from AVE4041 were the remains of a pair of trousers which had been close to the bomb. The label was intact. The manufacturer was traced to Malta and a clothing company called Yorkie, with a unique order supplied to Mary's House, Gauci's shop. Whatever the inconsistencies in Gauci's account, the clothes packed into the suitcase that sat alongside the bomb were bought at Mary's House. But the Crown's certainty that it was Megrahi who bought them is far from clear. Gauci's statements as to the dates when Malta's Christmas lights were on, and whether or not the purchases had been made when it was raining are key factors that placed Megrahi on the island at specific times. Again, this evidence has been shown to be inconsistent.

His identification of Megrahi was crucial to the verdict. However, the SCCRC acknowledged that if the payments to Gauci had been revealed, then this "was capable of affecting the course of the evidence and the eventual outcome of the trial". The review commission also found that three days before Gauci picked out the Libyan in a formal identification parade, he had held a magazine featuring an article on the Lockerbie bombing, complete with a picture of Megrahi as the culprit. In December 1988, Megrahi had indeed been in Malta. But it is hard to avoid the impression that Gauci's account of the man who bought the clothes that ended up inside the Samsonite suitcase was influenced by the prospect of a sizeable US reward.

The negotiations with Colonel Gaddafi that brought Megrahi and his co-accused, Lamin Khalifah Fhimah, to the Netherlands in 1999 involved Libya offering £8m in compensation to the victims' families. In return, the United Nations lifted sanctions that were crippling Libya's economy. Reward, blackmail or diplomatic and tribal trading? Whatever the true background, there is still a whiff of West and Middle East deal-making surrounding Lockerbie.

"If not Megrahi then who?" should be the question troubling Scotland's criminal justice system 25 years on, because those who brought down Pan-Am Flight 103 have still not been brought to justice. This anniversary, supposed to remember the innocent dead, is also marked by an ongoing shame – the pretence that a Scottish court got it right. It didn't. And as Martin Luther King said: "An injustice anywhere is a threat to justice everywhere."

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