The results of the Pearl Project, an investigation carried out by a team of American journalists and students and spanning more than three years, raise troubling questions about Pakistan's dysfunctional criminal justice system and underscore the limits U.S. officials face in relying on Pakistani authorities.
The four men convicted in the killing did help kidnap the American journalist, according to the investigation. But it says forensic evidence known as "vein-matching" bolsters the confession of al Qaeda No. 3 Khalid Sheikh Mohammed, the professed mastermind of the Sept. 11, 2001 attacks on the United States, to having killed Pearl.
The report says at least 14 of 27 people involved in abducting and murdered Pearl in 2002 are thought to remain free. And the four who have been convicted could be released if their appeal is ever heard because of false and contradictory evidence used in their trial.
Pearl, 38, was abducted from this southern port city on Jan. 23, 2002, while researching a story on Islamist militancy after the Sept. 11 attacks. On Feb. 21, 2002, a video of Pearl's killing was delivered to U.S. officials in Pakistan. His remains were found in a shallow grave on Karachi's outskirts three months later.
Within months of Pearl's disappearance, Ahmed Omar Saeed Sheikh, a British national of Pakistani heritage, and three accomplices were caught, charged, and convicted of murder and kidnapping. Sheikh, called the kidnapping's mastermind, was sentenced to death in July 2002. The three others were given life terms, which in Pakistan usually means 25 years.
Since then, the men's appeals have gone nowhere in the courts, despite dozens of hearings. Both the defense and the prosecution blame each other for stalling tactics. And there is constant speculation that Sheikh is being protected, possibly by Pakistani intelligence agencies.
Defense attorney Rai Basheer said the prosecution knows it would lose on appeal and is delaying the process, but prosecutor Raja Qureshi dismissed those claims.
"I challenge the defense to come and attend the case properly and consistently, and they will themselves know whose case is weak," Qureshi told The Associated Press.
The Pearl Project's findings appear to strengthen the defense's hand.
For instance, it finds significant discrepancies between Pakistani police reports and later court testimonies, including that of a taxi driver whose account was considered crucial to the conviction.
Authorities apparently cajoled the driver to change his earlier story and, while testifying, place Sheikh with Pearl near the restaurant where the journalist was picked up by his abductors, the report says. But Sheikh is believed to have left Karachi before other men he had recruited carried out the kidnapping.
At the same time they were building their case against Sheikh and the three others, investigators did not pursue leads provided by another suspect in custody. That man, Fazal Karim, allegedly was one of the guards holding Pearl hostage and was there during his slaying. Karim also led investigators to Pearl's grave.
But his account differed from the taxi driver's, thus threatening the prosecution's case against the four on trial. U.S. officials pushed the Pakistanis to restart the trial to include all the evidence, but the prosecutor argued that doing so would give the defense a huge advantage. So Karim's account didn't make it to court, and he was later set free.
The murder case against the four convicts also appears weakened by Mohammed's suspected role.
The al Qaeda No. 3 claimed after his capture that he beheaded Pearl. Mohammed is being held at the Guantanamo Bay U.S. military prison, and the confession is believed to have come during interrogation that included waterboarding.
But the Pearl Project reports that U.S. investigators also used a technique called "vein-matching" to compare a photo of Mohammed's hand with a photo of a hand shown on the video of Pearl's killing, and that it's a fit.
Vein-matching is not considered as reliable as methods such as fingerprinting, but the CIA and FBI do use it at times to identify suspects, the report says. It involves "extracting the information of the vascular structure of a hand or finger and converting it into a mathematical quantity."
One of the more gruesome findings of the report is that the videotaping of Pearl's beheading was initially bungled, and that the killing had to be re-enacted. Mohammed had already slashed Pearl's neck when the cameraman had to restart the taping. The second time, Mohammed fully severed the head.
Two of Mohammed's nephews may have been present during the killing, according to the report, which cites U.S. and Pakistani officials. One nephew, Ali Abdul Aziz Ali, is also at Guantanamo and is believed to have been the al Qaeda facilitator in Karachi for Richard Reid, the shoebomber who tried to destroy a trans-Atlantic flight in 2001. Pearl was trying to research the Reid case and track down his facilitator when he was kidnapped.
The report notes that neither Mohammed nor the detained nephew is likely to be charged in Pearl's killing because that could complicate cases against them over the Sept. 11 attacks. The other nephew's whereabouts are unknown.
How exactly al Qaeda became involved in the Pearl plot remains a mystery. The report cites Mohammed's interviews with FBI agents, in which he said he was directed to Pearl by another al Qaeda leader, Saif al-Adel. It also says that Pearl's murder was "the first known operation in which Pakistani militants collaborated with al Qaeda."
In Pakistan, all parts of the justice system - police, prosecuting agencies, defense lawyers and judges - are riddled with corruption and ineptitude. The conviction rate hovers between 5 and 10 percent, according to a report in December by the International Crisis Group. That report also noted that outsiders, including spy agencies, use intimidation to compromise the justice system.
Conspiracy theories have flourished in Pakistan about the relationship Pakistan's main spy agency, Inter-Services Intelligence, had with Sheikh.
As Pakistani officials were searching for him in 2002, Sheikh turned himself in to a former ISI official, Ejaz Shah, at the urging of his father and his uncle.
Yet it wasn't until a week later, on February 12, that U.S. officials learned that police had him, the report says. U.S. authorities told the Pearl Project that they have no idea what happened with Sheikh during those seven "lost days."
"Whether Sheikh sought refuge in Shah's custody because there was a family connection and would, therefore, provide a soft landing into the legal system, or whether it was because Sheikh had a long history with the ISI is still unresolved," the Pearl Project's report states.
The Pearl Project's sponsors include Georgetown University and the International Consortium of Investigative Journalists, a program at the Center for Public Integrity in Washington, D.C. The lead writer of the report was journalist Asra Q. Nomani, with whom Pearl and his wife were staying in Karachi when he was kidnapped.