His timing could not have been worse. Three months later, on 11 September, al-Qa'ida launched terrorist attacks in New York, killing 3,000 people and triggering the invasion of Afghanistan the following year.
As the US-led coalition and Northern Alliance forces swept through the country, Mr Mohamed, 30, fled across the border into Pakistan. His attempt to fly out of Karachi airport on a false passport brought him to the attention of the Pakistani security forces who delivered him into the hands of the Americans. His presence in Afghanistan and admission that he had attended military training camps made him, in the eyes of the CIA, a prime terror suspect.
As the war on terror gathered momentum, it seemed America was prepared to sanction torture to achieve its aims. Britain, according to Mr Mohamed's lawyer, simply turned a blind eye to their allies' unlawful practices. Details of the abuse Mr Mohamed underwent in Pakistan are contained in the "redacted" (blacked-out) section of the British High Court judgment on his case that the Foreign Secretary, David Miliband, is refusing to release, claiming that to do so would damage the intelligence-sharing relationship with America.
When an MI5 officer went to interrogate Mr Mohamed on 17 May 2002, Mr Mohamed claims he was made fully aware of what had been happening. In an interview given to the British media this month, Mr Mohamed described the agent, who he says gave his name as "John", as being aged about 30, about 5ft 10in, stocky and having short, black hair and a goatee.
He added: "There was another guy with him, about the same size with a full, dark beard. I don't know if he was British or American. The Americans had already been threatening to send me somewhere where I would be tortured far worse, like Jordan or Egypt. I was given a cup of tea and asked for one sugar. The other guy told me: 'You'll need more than one sugar where you're going.'"
He was quizzed about a "dirty bomb" plot and his knowledge of nuclear bomb websites. John dutifully recorded that he claimed the website was a joke. Mr Mohamed says: "John told me that if I co-operated he'd tell the Americans to be more lenient with my treatment." In a confidential memo John wrote: "I told Mohamed that he had an opportunity to help us and help himself. The US authorities will be deciding what to do with him and this would depend to a very large degree on his co-operation. ... If he persuaded me he was co-operating fully then ... I would explore what could be done for him with my US colleagues."
But it appears MI5 felt he wasn't fully co-operating. John's memo ended: "While he appeared happy to answer any questions, he was holding back a great deal of information on who and what he knew in the UK and in Afghanistan."
Mr Mohamed was flown – trussed, gagged, blindfolded and wearing a giant nappy – from Islamabad to Rabat in Morocco on 21 July 2002. He had, he said, already endured beatings at the hands of an interrogator named Marwan: "They cut off my clothes with some kind of scalpel. I was totally naked. I was afraid to ask Marwan what would happen because it would show fear. I tried to put on a brave face.
"They took the scalpel to my right chest. It was only a small cut. Then they cut my left chest. One of them took my penis in his hand and began to make cuts. He did it once, and they stood still for maybe a minute, watching my reaction.
"I was trying desperately to suppress myself, but I was screaming. Marwan seemed to smoke half a cigarette and start another. They must have done this 20 to 30 times in maybe two hours. There was blood all over. They cut all over my private parts. One of them said it would be better just to cut it off, as I would only breed terrorists."
This, Mr Mohamed says, was repeated many times in the next 15 months. Under torture, his confessions became ever more elaborate. "They had fed me enough through their questions for me to make up what they wanted to hear. I confessed to it all. There was the plot to build a dirty nuclear bomb, and another to blow up apartments in New York with their gas pipes."
Even after this treatment, papers disclosed to him for a US court case show that MI5 was colluding with his torturers. In late September 2002, one document reveals: "The Service received a report from the US of an interview of Mr Mohamed." On 30 September 2002, MI5 held a case conference about him with their US colleagues in London.
Mr Mohamed was "rendered" by the CIA again in January 2004 and taken to Afghanistan. "When I got to Kabul a female agent started taking pictures of my genitals. She was shocked. When they removed my diaper she could see blood was still oozing from the cuts on my penis. For the first two weeks they had me on antibiotics and they took pictures of my genitals every day."
Later that year Mr Mohamed was transferred to Guantanamo Bay where he was held for five years before his release last month.
Torture: The legal minefield
What laws may have been broken?
Aiding and abetting torture in the UK or overseas is an offence under the 1988 Criminal Justice Act. And Section 52 of the UK's International Criminal Court Act of 2001 provides for prosecution of anyone who "assists in concealing" a war crime, such as torture.
What is the maximum prison sentence for these offences?
Life imprisonment. But someone found guilty of complicity will draw a lesser sentence than a defendant convicted of the actual crime of torture.
What will the police investigation entail?
A team of senior police officers will interview the MI5 agent who questioned Binyam Mohamed in Pakistan. They may also speak to his superiors about any covert policy of colluding in CIA torture or engaging in a policy of deliberate ignorance of the facts.
Will the police investigation answer all the questions surrounding Britain's alleged collusion in torture?
No. The Metropolitan Police inquiry will focus on substantive criminal offences where there is hard evidence to link individuals to any alleged wrongdoing.
The political dimension of any covert policy on torture is unlikely to be uncovered. Yesterday Tory leader David Cameron was among those leading the calls for a much wider inquiry by a former judge or senior civil servant.
"As well as having this investigation by the Attorney General, we do need a more targeted and clear review to look at whether the right processes and procedures were in place," he said.
"I don't think the Government is doing enough to reassure Britain's good name and to get rid of this potential stain that hangs over us."
Will the American, Moroccan or Pakistani agents accused of carrying out the torture on Mr Mohamed ever face justice?
This seems more and more unlikely. None of these governments have disclosed the names of any agents involved in Mr Mohamed's various interrogations, which he claims took place between 2002 and 2004. Then-US president George Bush took no steps to prosecute anyone over the secret rendition programme. Nor has a change of US administration led to a change of policy. The only real prospect of a prosecution would be under war crimes legislation, which authorises the extradition of suspects who have not been dealt with by their own countries' judicial systems. A spokeswoman for Reprieve, the legal action charity that is representing Mr Mohamed, said: "If US personnel are found to be involved in these war crimes, they should be extradited to the UK for prosecution... they will clearly not be held accountable in the US."
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