Just when Fatima Bouchar thought it couldn't get any worse, the Americans forced her to lie on a stretcher and began wrapping tape around her feet. They moved upwards, she says, along her legs, winding the tape around and around, binding her to the stretcher. They taped her stomach, her arms and then her chest. She was bound tight, unable to move.

Bouchar says there were three Americans: two tall, thin men and an equally tall woman. Mostly they were silent. She never saw their faces: they dressed in black and always wore black balaclavas. Bouchar was terrified. They didn't stop at her chest – she says they also wound the tape around her head, covering her eyes. Then they put a hood and earmuffs on her. She was unable to move, to hear or to see. "My left eye was closed when the tape was applied," she says, speaking about her ordeal for the first time. "But my right eye was open, and it stayed open throughout the journey. It was agony." The journey would last around 17 hours.

Bouchar, then aged 30, had become a victim of the process known as extraordinary rendition. She and her husband, Abdel Hakim Belhaj, a Libyan Islamist militant fighting Muammar Gaddafi, had been abducted in Bangkok and were being flown to one of Gaddafi's prisons in Libya, a country where she had never before set foot. However, Bouchar's case is different from the countless other renditions that the world has learned about over the past few years, and not just because she was one of the few female victims.

Documents discovered in Tripoli show that the operation was initiated by British intelligence officers, rather than the masked Americans or their superiors in the US. There is also some evidence that the operation may have been linked to a second British-initiated operation, which saw two men detained in Iraq and rendered to Afghanistan. Furthermore, the timing of the operation, and the questions that Bouchar's husband and a second rendition victim say were subsequently put to them under torture, raise disturbing new questions about the secret court system that considers immigration appeals in terrorist cases in the UK – a system that the government has pledged to extend to civil trials in which the government itself is the defendant.

This year, the Crown Prosecution Service announced police had launched an investigation into the "alleged rendition and alleged ill-treatment" of Bouchar and Belhaj, and a second operation in which a Libyan family of six were flown to one of Gaddafi's prisons.

It appears inevitable that Scotland Yard's detectives will want to question the man who was foreign secretary at the time – Jack Straw.

Ten years before Bouchar's abduction and rendition, many of her husband's associates had been permitted to settle in Britain. These men were members of al-Jama'a al-Islamiyyah al-Muqatilah fi-Libya, the Libyan Islamic Fighting Group (LIFG), an organisation formed in the early 1990s and dedicated to Gaddafi's removal. The LIFG was not banned in the UK, and its members appear to have found the country a convenient place to gather and raise funds. There were even reports – officially denied – that MI6 encouraged the LIFG in an unsuccessful attempt on the dictator's life.

But from 2002 the UK ceased to be such a safe haven for the LIFG. The US and UK governments were beginning to repair their relations with Gaddafi, a rapprochement that would soon see him abandon his WMD programme and open his country's oil and gas reserves to western corporations.

Held by armed police

One Thursday evening in November that year, a 36-year-old LIFG member who was living in London was arrested by armed police as he attempted to board a flight at Heathrow. He was told he was being detained under the Anti-terrorism, Crime and Security Act, a piece of legislation that had been rushed on to the statute books within weeks of 9/11, and which allowed the British government to detain international terrorism suspects without trial. From that moment the man was anonymised, by court order – in part to protect his relatives in Libya – and could be referred to only as "M".

When M had arrived in the UK as an asylum seeker eight years earlier, he had readily told Special Branch detectives that he was a member of the LIFG. On his arrest at Heathrow he insisted that the organisation had no connection with international terrorism and was concerned only with the removal of Gaddafi. After being detained at Belmarsh high security prison in south-east London, M appealed to the Special Immigration Appeals Commission (SIAC), a tribunal that allows the government to give evidence in secret, unseen by the appellant or the appellant's lawyers.

Abdel Hakim Belhaj in Tripoli in August 2011 where he was the rebel military leader. He had been detained in 2004 in Bangkok and rendered to Libya with his pregnant wife Fatima Bouchar. Photograph: Francois Mori/AP

In March 2004, M became the first and only person detained under the act to win an appeal at SIAC. The tribunal accepted that there were no links between LIFG and al-Qaida, and criticised the Home Office for its "consistent exaggeration" of M's alleged links with members of al-Qaida. As the law permitted only "international terrorists" to be detained without trial, and not domestic insurgents, M was set free. A few days after SIAC's decision, notice was passed to the Home Office and MI5, and Fatima Bouchar and her husband were detained in Bangkok.

Bouchar's husband made no secret of being a leading member of the LIFG. That year, the couple had left China, where they had been living in exile, and attempted to travel to the UK via Malaysia. When they were detained in Kuala Lumpur and questioned about Belhaj's false Iraqi passport, an acquaintance went to the British high commission to explain that the couple were attempting to reach London. Shortly after this, they were told that they would be permitted to travel to the UK on a BA flight, despite not having EU passports or UK visas. But when the aircraft stopped off at Bangkok, the pair were detained and taken to a US-run detention facility.

It was known that the CIA had been operating a secret prison in Thailand since 9/11, but its precise location was unknown. Bouchar and Belhaj arrived there within minutes of being detained, suggesting that it was located within the perimeter of Don Muang international airport. They were immediately separated.

Belhaj says he was blindfolded, hooded, forced to wear ear defenders, and hung from hooks in his cell wall for what seemed to be hours. He says he was severely beaten. The ear defenders were removed only for him to be blasted with loud music, he says, or when he was interrogated by his US captors.

Bouchar says that when she was dragged away from her husband she feared he was going to be killed. "I thought: 'This is it.' I thought I would never see my husband again ... They took me into a cell, and they chained my left wrist to the wall and both my ankles to the floor. I could sit down but I couldn't move. There was a camera in the room, and every time I tried to move they rushed in. But there was no real communication. I wasn't questioned." Bouchar found it difficult to comprehend how she could be treated in this way: she was four-and-a-half months pregnant. "They knew I was pregnant," she says. "It was obvious." She says she was given water while chained up, but no food whatsoever. She was chained to the wall for five days. At the end of this period she was taped to the stretcher and put aboard the aircraft, unaware of where she was going or whether her husband was on board. At one point the aircraft landed, remained on the ground for a short period and then took off again. Only when it landed a second time did she hear a man grunting with pain, and realise her husband was nearby.

Belhaj says he had been shackled to the floor of the plane, with his hands chained to his feet in a manner that made it impossible either to sit or lie down. Sometimes his grunts would be met with a kick; on other occasions, he says, a cushion would be placed under his elbows, giving him temporary respite before it was taken away again.

The plane touched down at Tripoli with its cargo still trussed up; a gift, apparently, to the regime they had hoped to overthrow. The pair were driven separately to Tajoura prison, east of the city, and Bouchar was led to a cell where she would spend the next four months. Initially, she was interrogated for around five hours a day. "At one point a cot was brought in the cell along with some baby clothes, nappies, a bed cover and a baby bath," she says. "I really thought I was going to have to have my baby there, and that we would both be held there.

Bouchar was released shortly before giving birth to a son, apparently because word of her husband's capture had reached the outside world. Belhaj was brought to her cell for a few moments, and then she was set free, though not permitted to leave the country.

Two weeks after the couple were rendered to Libya, Tony Blair paid his first visit to the country, embracing Gaddafi and declaring that Libya had recognised "a common cause, with us, in the fight against al-Qaida extremism and terrorism". At the same time, in London, the Anglo-Dutch oil giant Shell announced that it had signed a £110m deal for gas exploration rights off the Libyan coast.

Three days after that, a second leading LIFG member, Abu Munthir al-Saadi, was bundled aboard a plane in Hong Kong and taken to Tripoli in a joint British-Libyan rendition operation. Saadi's wife and four children were also kidnapped and taken to Libya. The youngest was a girl aged six. The family was incarcerated at Tajoura for more than two months before being released. Saadi and Belhaj were held for more than six years, however, and say they were subjected to torture throughout this time.

At one point, they say, early in their incarceration, they were interrogated by British intelligence officers after being tortured by the Libyan captors. These visitors wanted to learn more about LIFG members living in the UK. The two men say their torturers had made clear that their treatment would improve if they told the British that these LIFG activists were linked with al-Qaida: something that SIAC had ruled, just weeks earlier, was not the case.

The flight plan for the 2004 rendition operations found in Moussa Koussa's office.

The role that MI6 played in arranging the rendition of these two Libyan dissidents and their families is now well known, thanks to a discovery made last September by Peter Bouckaert, a director with Human Rights Watch, inside the abandoned office of Moussa Koussa, Gaddafi's foreign minister and former intelligence chief. Bouckaert found a file containing hundreds of secret letters and faxes that MI6 and the CIA had sent to Koussa during the early days of the rapprochement between Libya and the west. Among them were a series of documents detailing the 2004 rendition operations.

A close examination of those papers show that a great deal of planning went into the operations, withMI6 informing Koussa's office as early as November 2003 that they were seeking the assistance of Chinese intelligence officers in their attempt to deal with "the Islamic extremist target in China". When MI6 learned that Belhaj was being held in Malaysia under his nom de guerre, Abdullah al-Sadiq, along with his pregnant wife, they were quick to tip off Tripoli.

Notoriously, perhaps, one fax from Mark Allen, then head of counter-terrorism at MI6, congratulated Koussa on the "safe arrival" of Belhaj – "the least we could do for you and for Libya" – and referred to an "amusing" request by the CIA that anything the dissident said under interrogation should be passed first to them.

"I know I did not pay for the air cargo," Allen says: but after all, the intelligence that led to the couple's rendition was British.

Another fax, sent by the CIA two days before Blair's visit, with a cover sheet marked "rendition of Abu Munthir", shows the US to be eager to join and finance that operation after learning that MI6 and Gaddafi's government were about to embark upon it. Also buried away inside the secret document cache is a fax that shows MI6 felt itself not to be bound by the anonymity order imposed after M had been detained under the Anti-Terrorism, Crime and Security Act in November 2002. The following January, the intelligence service sent Koussa what it described as an MI5 "intelligence resumé", detailing M's full name and date of birth and disclosing that he was an active member of the LIFG. The fax also listed the Libyan telephone numbers called by M. It was being sent, MI6 explained, "for research purposes and analysis purposes".

By piecing together records of air traffic control logs and matching them with a document found in the Tripoli cache, it is possible to trace the route taken by the aircraft that rendered Bouchar and Belhaj from Bangkok to Tripoli in March 2004. There are a couple of surprises along the way. The aircraft was a Boeing 737 with the tail number N313P, operated by a North Carolina company called Aero Contractors, which has been widely reported to be a CIA front.

N313P is now known to have been used in a great many rendition operations: it was one of the aircraft that carried a shackled and hooded Binyam Mohamed, for example.

According to the records of the European air traffic management agency, Eurocontrol, and the Federal Aviation Administration in the US, N313P took off from Dulles airport in Washington DC at 2.51am on 7 March 2004, landing at Misrata in Libya shortly after noon local time. When N313P departed from Misrata, it flew beyond Eurocontrol's area of responsibility, and disappears, temporarily, from its records.

But a flight plan had been prepared by the CIA the previous day, and faxed to Libya, where it was found among the secret cache of letters and faxes recovered from Koussa's office. This document shows that after leaving Libya, the rendition aircraft planned to stay overnight on the Seychelles before continuing to Bangkok. It was then due to leave Bangkok on the evening of 8 March, the date that Bouchar and Belhaj were forced on board an aircraft.The CIA flight plan shows that the aircraft was then due to fly to Tripoli via Diego Garcia, where it would refuel during the early hours of 9 March.

Any evidence that the rendition plane landed on Diego Garcia would be enormously damaging for the British government. Although the remote coral atoll in the Indian Ocean is operated as a US military outpost, it is a British Overseas Territory, and the UK is legally responsible for events there.

The last Labour government was highly sensitive to reports that Diego Garcia played a part in the global rendition programme. Both Blair and Straw insisted on a number of occasions that there was "no evidence" for this. Those assurances proved to be wrong: in February 2008, amid mounting evidence that rendition aircraft had landed on the atoll, David Miliband, one of Straw's successors at the Foreign Office, told the Commons that he was "very sorry indeed" to report that two rendition flights had refuelled there in 2002.

By way of reassurance, Miliband told MPs that no prisoners had been allowed to disembark while the aircraft were refuelled, and that "US investigations show no record of any other rendition through Diego Garcia or any other overseas territory, or through the UK itself, since then".

Diego Garcia question

When the CIA flight plan was recovered from Koussa's office, the Guardian asked the Foreign Office whether the plane carrying Bouchar and Belhaj had indeed stopped off on Diego Garcia, despite Miliband's assurances. The department sought initially to imply that the aircraft had been refused permission to land, but would not answer the question directly. Asked for a yes-or-no answer, a spokeswoman declined.

In any case, by the evening of 9 March, N313P had reappeared on the radar of Eurocontrol. The agency's records show the aircraft landed once more at Misrata airport: the exact place that the CIA flight plan said it would be.

On board were Bouchar, taped to her stretcher, and Belhaj, still shackled in an excruciating stress position at the end of their 17 hour flight.

With its prisoners rendered and the Libyan mission accomplished, N313P left for Palma de Mallorca. Hotel records from the five-star Gran Melia Victoria, a favoured destination for rendition teams, show that the crew of 10 men and three women booked in for two nights of rest and recreation.

Curiously, however, when the aircraft left Palma on the evening of 11 March, it did not return to the US. Instead, it flew east to Baghdad. After less than two hours on the ground in Baghdad, it departed for Kabul. N313P remained in Kabul for 24 hours, then flew back to Washington via Larnaca on Cyprus and Shannon on the west coast of Ireland.

The flight to Kabul appears to coincide with another British-initiated operation, one that saw two more people being subjected to extraordinary rendition, this time from Iraq to Afghanistan.

Yunus Rahmatullah and Amanatullah Ali were two Pakistani men suspected of having travelled to Iraq to fight for al-Qaida. MI6 is understood to have tracked them as they travelled across Iran and into Iraq, and when they arrived at a house in southern Baghdad, a decision was taken to raid the building, a mission codenamed Operation Aston.

SAS troopers attacked the house in late February, shooting dead two men and capturing several others. After the detainees were handed over to the US military, Rahmatullah and Ali were held at a prison at Baghdad international airport, according to a British military source. Then they were flown to Afghanistan and taken to the US-run prison at Bagram, north of Kabul, a transfer that was in breach of the Geneva conventions. They remain at Bagram today, despite an attempt to secure the release of Rahmatullah by persuading the appeal court in London to grant a habeas corpus writ.

The SAS troops who took part in Operation Aston were members of a joint US-UK special forces task force that rounded up large numbers of people in Iraq, missions in which the US was, on every other occasion, deemed legally to be detaining authority. But former members of the taskforce say Operation Aston was an all-British affair, and they were never sure why.

The Guardian has asked the Foreign Office on several occasions whether N313P flew Rahmatullah and Ali to Afghanistan, but the department has always failed to answer.

The following year, 2005, the LIFG was banned in the UK, and a number of its members, including M, were arrested. The Home Office said it had taken this step because it had come to the conclusion that the group was "part of the wider global Islamist extremist movement, as inspired by al-Qaida". To what extent this assessment drew upon intelligence provided by Gaddafi's government – including statements made by LIFG prisoners under interrogation – remains unclear.

What is becoming clear, however, is that the rendition of Abdel Hakim Belhaj and Abu Munthir al-Saadi had a number of unintended consequences.

By early 2005, the British government had been forced to conclude that the capture of the more moderate elements among the LIFG leadership, such as Belhaj and al-Saadi, had resulted in a power vacuum that was being filled by men with pan-Islamist ambitions. Among a number of documents found in a second Tripoli cache, at the British ambassador's abandoned residence, was a secret 58-page MI5 briefing paper that said "the extremists are now in the ascendancy," and that they were "pushing the group towards a more pan-Islamic agenda inspired by AQ [al-Qaida]".

The realisation that MI6 had passed M's name and information about his contacts to Gaddafi's notorious intelligence agencies, despite the existence of an order seeking to preserve his anonymity, provoked outrage among lawyers who work within the SIAC system.

There was also dismay at the manner in which the rendition operations were mounted shortly after SIAC had ruled that there were no links between the LIFG and al-Qaida. M's lawyer, Gareth Peirce, believes that to be one of the reasons the two men were taken to Libya. "The UK's complicity in the renditions of Belhaj and Abu Munthir is sickening," Peirce says. "Their synchronisation with the obtaining of perceived missing 'intelligence' for domestic proceedings damns both enterprises equally."

Last December, the attorney general, Dominic Grieve, wrote to the head of Scotland Yard, Bernard Hogan-Howe, drawing his attention to the two rendition operations. A few weeks later the Yard announced it was mounting a criminal investigation, which is continuing.

Meanwhile, no attempt is being made to deny MI6 involvement in the renditions: instead, well-placed sources say the operations were "ministerially authorised government policy". This has led to reports that police will need to interview Jack Straw.

The Guardian has repeatedly put a number of questions about the renditions to Straw, asking whether he authorised the operations and, if not, which minister was responsible; the former foreign secretary has repeatedly declined to answer.

A further consequence is that lawyers representing the rendition victims are suing MI6, MI5, the foreign office, and Mark (now Sir Mark) Allen. Belhaj – who was released from prison along with Saadi in 2010 – led the militia that drove Gaddafi's forces out of Tripoli last year, and is now settled in the city with Bouchar. They embarked on legal proceedings only after the UK government declined to offer them an apology.

Bouchar appears to remain deeply traumatised by her abduction and imprisonment, and that of her husband. "The time around the birth of a first child should be among the happiest in a couple's lives," she says, "but it is very difficult for me to look back at that time because I wanted to die rather than be going through what I did."

Happily, she is now pregnant with the couple's second child.

Asked whether it wished to say anything that would help explain the UK government's role in the rendition operations, the Foreign Office declined to comment.

The justice ministry, meanwhile, is pressing ahead with proposed legislation that would introduce SIAC-style secrecy to any civil trial or inquest in which a minister has decided that some evidence is too sensitive to be aired in public.

Bouchar's lawyers condemn not only her mistreatment, but the plans to force litigation on her behalf into secret court hearing.

Sapna Malik, of the law firm Leigh Day, says: "Fatima's utterly barbaric treatment, and Britain's role in it, must come under the full scrutiny of an open court and not be condemned to a secret chamber."

Cori Crider of the legal charity Reprieve, which is also representing her, added: "It is bad enough that MI6 and the CIA had Abdel Hakim Belhaj tortured, when his only opponent was Colonel Gaddafi, but it is impossible to see what they hoped to achieve by kidnapping his pregnant wife, taping her up and forcing her on a plane back to Libya.

"Instead of saying sorry, the security services are busily trying to shunt Fatima's case and those like it into secret. Make no mistake: when Ken Clarke says a 'tiny' category of national security cases will be heard in closed court, it is Fatima, taped to the stretcher, he and those behind him have in mind."