A friend's labour of love reveals who killed Daniel Pearl

Nine years after the journalist Daniel Pearl was kidnapped and beheaded by al-Qa'ida militants, a new inquiry has concluded he was almost certainly killed by Khalid Sheikh Mohammed, the man currently in US custody and accused of plotting the 9/11 attacks. The investigation also found that of 27 men connected with the killing, more than half remain at large.

Highlighting fresh concerns about the efficacy of Pakistan's police and legal system, the independent investigation carried out by American journalists found that the four men who were convicted for the reporter's murder were not actually present when he was killed. In one of its most gruesome conclusions, the inquiry also said that when 38-year-old Mr Pearl's throat was cut, the kidnappers' video camera was not running so the act was carried out a second time and on that occasion he was decapitated and his head held aloft.

The three-year investigation into the killing of Mr Pearl was led by a friend and colleague, Asra Nomani, with whom the journalist and his wife were staying in Karachi when he was abducted in January 2002. Speaking yesterday from her current home in West Virginia, she described the inquiry as a "labour of love".

"The thing I found the most shocking was that so many people were involved and so many remain free," she said. "It also hurts... that not one had the act of conscience to halt this crime and to give some help to Danny."

Since Mr Pearl was murdered, there has been uncertainty over who was responsible for his actual killing. In 2002, Ahmed Omar Saeed Sheikh and three other men were convicted of the murder, a conviction that the British-born Sheikh, who was sentenced to death, is appealing against.

Then in 2007, Khalid Sheikh Mohammed, the man who has described himself as the mastermind of the September 11 attacks, told a military hearing at Guantanamo Bay that he had personally beheaded Mr Pearl and ordered that a copy of the video of the incident be dispatched to the US consulate in Karachi.

"I decapitated with my blessed right hand the head of the American Jew, Daniel Pearl, in the city of Karachi, Pakistan," he is said to have told the closed hearing. The full details of his confession are classified.

Some security experts raised questions about the veracity of his statements. It has emerged that Mohammed was waterboarded by interrogators and also claimed to have been behind other plots, including an attack on Big Ben. Crucially, the video that shows Mr Pearl's murder, easily accessible on the internet, does not show the face of the killer.

However, the inquiry by Ms Nomani and journalism students at Georgetown University, based on hundreds of interviews and the examination of court documents, says US investigators have used a technique called "vein-matching" to compare a photograph of Mohammed's hand with the hand of the killer shown in the video. While the method is not considered as reliable as fingerprinting, the inquiry says US investigators believe the two are a match.

The report by the Pearl Project, supported by the US-based Centre for Public Integrity, does not make clear precisely how Mohammed came into contact with Sheikh and the other kidnappers, who apparently seized Mr Pearl to ransom him.

But they say Mohammed received instructions from Saif al-Adel, an Egyptian and senior al-Qa'ida figure who is still at large. Mohammed and two other men then arrived at the compound on the outskirts of Karachi where Mr Pearl was being held. The arrival of the al-Qa'ida men effectively sealed the reporter's fate. The nexus between foreign al-Qa'ida fighters and home-grown militants in Pakistan is now well documented, but the inquiry claims the kidnap and killing of the reporter was the first example of it in action.

Mohammed, who was seized in a pre-dawn raid in the Pakistani city of Rawalpindi in March 2003, later told FBI interrogators that he went ahead with the murder to further raise the profile of al-Qa'ida. "I wanted to make sure that I got the death penalty," he said. Officials believe that two of Mohammed's nephews may have been involved in the killing and even filmed the beheading. One of them, Ali Abdul Aziz Ali, is also being held at Guantanamo Bay while the other remains at large.

Mr Pearl was abducted while pursuing inquiries into Richard Reid, the British shoe-bomber and his possible facilitators in Pakistan. He was lured to what he believed was a meeting with a radical cleric and then seized. The dismembered remains of the reporter for The Wall Street Journal were discovered several months later after a tip-off from a man in custody, Fazal Karim. Pakistani Police had decided to build a case against Sheikh and the three other men and declined to fully pursue Karim's testimony, even though he may have been present at the murder and could have pointed the finger at Mohammed.

It is unlikely Mohammed or his nephew will be tried for the murder of Mr Pearl. US officials have decided it would complicate his prosecution over the plotting of the September 11 attacks. There is also concern that defence lawyers would seize on the fact he endured waterboarding. Mr Pearl's mother, Ruth Pearl, told the inquiry: "Justice wasn't served."

The kidnap and killing of Mr Pearl – portrayed in the film A Mighty Heart in which his widow, Mariane, was played by Angelina Jolie – continues to reverberate in Karachi, in the US and in Europe, where Mrs Pearl is bringing up the couple's son, Adam. Ms Nomani said she and her team had been driven both by the need to try and solve some of the unanswered questions and because of their friendship.

"The Pearl Project reveals that justice was not served for Danny," she said. "We couldn't save him, but we have uncovered the truth left behind. Through his death, Danny teaches us important lessons about the reality on the ground in Pakistan regarding militancy, Islamic extremism and terrorism."