Robert Fisk: The secret links, the missing evidence, and the questions that still have to be answered

Death will be by hanging. But Daniel Pearl's convicted murderer had his own threat for the secret Pakistani court which sentenced him yesterday for the murder of The Wall Street Journal reporter. "I will see whether who wants to kill me will kill me first, or get himself killed,'' Ahmed Omar Saeed Sheikh told Judge Ashraf Ali Shah in the basement of Hyderabad Prison. "I fought this case just to please my father ... I have said this before, this entire trial is a waste of time ... it is a decisive war between Islam and infidels....''

But the British-born prisoner's death threat was only the most bizarre episode in a very odd and very unique and – so the defence has constantly claimed – a very unfair trial. It was held in secret, in the bunker beneath Hyderabad Prison. No reporters were allowed to witness the 13 weeks of proceedings. The body, said to be that of Mr Pearl, was dug up in a Karachi slum on 17 May but has never been formally identified. Even the results of the DNA analysis of the remains has stayed secret. DNA samples were sent to both Pakistani laboratories in Lahore and the United States. Yet neither the Pakistanis nor the Americans has told us what they found. Why not?

Few Westerners, of course, doubt that Omar Sheikh was involved in Daniel Pearl's murder, although he was already in custody when the American consulate received a videotape which showed an anonymous hand cutting the reporter's throat with a knife. A cab driver even claimed that he saw Mr Sheikh drive off from a Karachi restaurant with Mr Pearl on 23 January when the journalist was researching an article on Islamic extremism – although the driver later retracted his evidence. Three other men charged with Mr Sheikh were sentenced to 25 years in prison. One of them, Fahad Naseem, had a laptop computer from which, according to FBI agents, he sent email pictures of Mr Pearl, trussed up in a tracksuit with a gun to his head.

Six other men – presumably including the throat-slitter – remain at large.

But Mr Sheikh's lawyer, Moshin Imam, argued against the verdict on grounds of illegal court procedures rather than his client's innocence. The judge had been shown the videotape of Mr Pearl's murder but in Pakistani law, according to Mr Imam, a videotape cannot be played in court without the presence of the man who made it – an impossibility when the actual murderer has yet to be apprehended. Mr Sheikh was held in illegal custody before being allowed access to a lawyer, Mr Imam said, which gave the police time to beat him into a confession. He was condemned only because Pakistan wanted to appease the United States.

Yet Mr Sheikh's courtroom death threat – not mentioned was his involvement in the kidnapping of three Britons in India in 1994 and his liberation from prison after the hijacking of an Air India airliner to Kandahar five years later – suggests that he was doing a lot more than his father, Saeed, claimed: organising a welfare group which provided clothes for the poor. He, too, claimed that the US, which supported Afghan fighters in their war against the Soviet Union, had ordered the conviction. "These holy warriors used to be the apple of their eye,'' he said. "Now they are rotten apples.''

Fear lay heavily over the court even before Mr Sheikh's chilling threat to the judge. The trial was held in Hyderabad – 200 miles from Karachi – for fear that the prosecutors might be assassinated. Forensic scientists initially refused to attend the exhumation of the court in Karachi on 16 May for fear that they, too, would later be murdered. The burial site was in a nursery garden in Sohrab Goth, a suburb inhabited by thousands of Afghan refugees.

What they found was almost as gruesome as the videotape. A Pakistani police source said gravediggers found the corpse had been dismembered into 10 parts. It was lying on its back with the severed head placed in an upright position on the base of the neck. The arms were severed from the shoulders, both legs had been amputated at the hips and were cut apart at the knees. The left foot had also been separated at the ankle joint. Inside the grave, the police also found three pieces of green rope, anti-diarrhoea pills, two car seats, three blood-stained plastic bags and a piece of cloth that may have come from the tracksuit Mr Pearl was wearing in the emailed pictures.

Pakistani pathologists estimated the man was killed on 29 or 30 January – at least five days before Mr Sheikh was arrested.

Mr Imam is appealing the death sentence. For his part, the Pakistani prosecutor, Raja Qureshi, is appealing the leniency of the 25-year sentences and demanding death for the other three men. But Pakistani law moves in mysterious ways. It could take at least 18 months for appeals to the High Court to be heard, although Pakistani authorities were hinting yesterday that all might be concluded within a fortnight. The Americans wanted Mr Sheikh extradited and were anxious to interrogate him about his contacts with al-Qa'ida. The request was refused by Pakistan. Some suspect they know the reason: because Mr Sheikh might tell the Americans about the links between al-Qa'ida and Pakistan's own intelligence organisation.