Ayaan Hirsi Ali was stabbed into the world's consciousness three years ago. One wet afternoon in November 2004, her friend Theo van Gogh – a film-maker, and descendant of Vincent – left his house and was about to cycle off through Amsterdam. But a young Dutch-born Muslim called Mohammed Bouyeri was waiting for him – with a handgun and two sharpened butcher's knives.

Wordlessly, he shot Van Gogh twice in the chest. Van Gogh howled: "Can't we talk about this?" Bouyeri ignored his pleas and fired four more times. Then he pulled out a knife and slit Van Gogh's throat with such strength that his head was almost severed from his body. He used the other knife to stab a five-page letter on to Van Gogh's haemorrhaging corpse.

Ayaan explains: "The letter was addressed to me." It said that Van Gogh had been "executed" for making a film with her that exposed the widespread abuse of Muslim women. Now, she would be "executed" too – for being an apostate.

Download the new Independent Premium app Sharing the full story, not just the headlines

She says that, even now, "every time I close my eyes, I see the murder, and I hear Theo pleading for his life. 'Can't we talk about this?' he asked his killer. It was so Dutch, so sweet and innocent." At the trial, Bouyeri spat at Van Gogh's mother: "I don't feel your pain. I don't have any sympathy for you. I can't feel for you because I think you're a non-believer."

This is the story of how a 25-year-old bogus asylum-seeker from Africa came to Europe in search of freedom – only to be nearly murdered here by a Dutchman, on the streets of Amsterdam, for speaking out against religion. The story opens in the blood-strewn streets of Somalia, and it closes amid the shiny white marble of Washington, DC – yet it also ends where it began: with Ayaan's life in danger. This is the story of the refugee who rocked Islam.

****

Her light, slight figure walks into the room so quietly that I would not have noticed her. But then the bodyguards follow: big, with their eyes darting into every corner in search of the long-awaited assassin, and you realise – yes, she is here. The internet is littered with pledges to torture and slay Ayaan Hirsi Ali. Yet, just a few weeks before we meet in London, the Dutch government has stripped away her security detail. She is paying for her own bodyguards now – and she could soon run out of cash.

So how did this soft-voiced woman come to be so hated – and to be abandoned by the country that gave her sanctuary?

The life of her mother hangs over Ayaan as a morality tale, a warning of what she might have been. "I was determined to never let what happened to my mother happen to me," she says, looking away. "I think that has made me the way I am."

By the time her mother gave birth to Ayaan in a hospital on the outskirts of Mogadishu in 1967, she was a broken woman. Like all Somalian women, she had been pressured all her life to suppress her personality, to sublimate everything to men and to God – to become what Ayaan calls "a devoted, well-trained work-animal".

In her youth, her mother had moments when she fought back, briefly and bravely. She insisted on leaving her family. They were desert nomads, in effect living in the Iron Age, with no writing, few metal objects, and a belief that Allah's angels and demons were constantly tinkering with reality. At 15, she walked out of their desert to the city of Aden.

Daily coronavirus briefing No hype, just the advice and analysis you need Enter your email address Continue Continue Please enter an email address Email address is invalid Fill out this field Email address is invalid Email already exists. Log in to update your newsletter preferences Register with your social account or click here to log in I would like to receive morning headlines Monday - Friday plus breaking news alerts by email Update newsletter preferences

But when her father called her back to be married to a man she had never met, she submitted. There was another flickering moment of freedom: exceptionally for that time and place, she later insisted on a divorce, and got one.

But this was all gone when Ayaan was born. The woman striving for independence had soon remarried, and crashed into the sheer weight of cultural expectation. She had been persuaded that "God is just and all-knowing and will reward you in the hereafter for being subservient". Her personality became deformed by it.

"She remained completely dependent," Ayaan says. "She nursed grievances; she was resentful; she was often violent, and she was always depressed." She would take it out on Ayaan, tying her arms behind her back and lashing her with wire for the slightest misdemeanour.

When Ayaan first menstruated, her mother screamed at her: "Filthy prostitute! May you be barren! May you get cancer!" Ayaan tried to commit suicide not long after. But now she says she knows that "all the abuse wasn't really directed at me, but at the world, which had taken her rightful life away."

When her second husband left her, Ayaan's mother was too infantilised to react. "It never occurred to her to go out and create a new life for herself, even though she can't have been older than 35 or 40 when my father left," Ayaan has written.

She remembers waking up every night as a small girl to hear her mother wailing. Once, she went into her mother's bedroom and placed a hand on her cheek; her mother screamed and beat her. After that, Ayaan would simply crouch at the door, listening to the wails, wishing she knew what to do.

Somali culture began to demand that Ayaan too become a submissive woman who scrubbed away her own personality and sexuality. When she was five years old, she was made "pure" by having her genitals hacked out with a knife. It was a simple process; her grandmother and two of her friends pinned her down, pulled her legs apart, and knifed away her clitoris and labia. She remembers the sound even now – "like a butcher, snipping the fat off a piece of meat". The bleeding wound was sewn up, leaving a thick tissue of scars to form as her fleshy chastity belt. She could not walk for two weeks.

Ayaan soon realised that, in a culture so patriarchal that it could not tolerate the existence of an unmaimed vagina, "I could never become an adult. I would always be a minor, my decisions made for me. But I wanted to become an individual, with a life of my own."

By reading novels, she heard whispers of a world where this was possible. For her, even poring over Enid Blyton and Barbara Cartland seemed transgressive, because they depicted a world where boys and girls played together on the basis of equality, and where women chose their husbands rather than having them forced on them by their fathers. Imagine a world so patriarchal that Barbara Cartland seems like a gender revolutionary.

Yet, on the road to this self-determining life, Ayaan turned first to its polar opposite: the very Islamic fundamentalism that now wants to kill her. Ayaan was taught from infancy to revere the Prophet Mohamed and the Koran, and she believed it all. She desperately wanted to please Mohamed, and his path seemed to her the only one.

So, once her family had moved to Kenya, a country where few people wore the headscarf, she chose to don one. She has written: "It had a thrill to it, a sensuous feeling. It made me feel powerful: underneath this screen lay a previously unsuspected, but potentially lethal, femininity. It sent out a message of superiority: I was the one true Muslim."

She began to go to a prayer group where the texts of Sayyid Qutb and Hassan al-Banna – the intellectual inspirations for al-Qa'ida – were pored over. When the Ayatollah Khomeini declared that Salman Rushdie should be murdered for what a maniac says in one of his novels, Ayaan wanted him dead. "I supported it," she says now, "and the logic of my position is that I would have become a martyr myself, or supported the people [who did become martyrs]."

What would that girl, who took to the streets to call for Rushdie's death, say if she could see you now? Would she think you should be killed too? For the first time in our interview, Ayaan pauses. A long pause. "What would that girl of 1989 think of this girl?" she repeats. "I think... well... people change." Another pause. "She would at least approve of it. That's why I try to explain – there is a reason why so many Muslims are silent when, in the name of Islam, violence is committed. It's because we believe that jihad is the sixth obligation. Those, then, who are brave enough to commit acts of jihad must deserve our commendation."

Then, one day, as she slid into jihadism, her absent father reappeared and announced that he had found her a good husband. Ayaan thought the potential life-partner stupid and ugly – but she had no choice. He was from the right clan, he had the right fundamentalist beliefs, and he wanted her. She knew what was expected: "A Muslim girl does not make her own decisions or seek control."

****

But she could not – would not – do it. She ran. She ran all the way to the Netherlands, on a plane, to claim asylum. She was terrified when she landed in the heartland of The Infidel. She expected to find depravity on every corner. But she was amazed. Here was a peaceful land that seemed like Paradise.

"In the Netherlands, I saw people we called infidels living an amazing life – men and women mixing, gay people being free, you could say whatever you wanted," she says. "Then I went back to the asylum-seekers' centre and almost everyone was from a Muslim country begging for the charity of these infidels. And I thought, 'If we're so superior, why are we begging from them?'"

She experimented in stepping out on to the streets without her hijab, expecting she would be harassed and raped by the sex-crazed infidel. Nobody looked twice. She began to test other democratic freedoms. She drank alcohol, she found a boyfriend – and she headed for the library to discover the principles that had created this place. She began to pore over the works of Enlightenment philosophy.

"Sometimes, it seemed as if every page I read challenged me as a Muslim. Drinking wine and wearing trousers was nothing compared to reading the history of ideas," she says. "The Enlightenment cut European culture from its roots in old fixed ideas of magic, kingship, social hierarchy and the domination of priests, and regrafted it on to a great strong trunk that supported the equality of each individual and his right to free opinions and self-rule." She found that all this was a profound challenge to the severe Islam she had been pickled in since childhood.

She began to study for a political science degree and was slowly rethinking her faith when, one bright morning in September 2001, the island of Manhattan became swathed in smoke. The chief hijacker, Mohammed Atta, was exactly the same age as Ayaan. She feels like she knows him, and that if her life had taken a different turn – if she had stayed in Kenya, with the jihadis – "perhaps I could have done it." And she says something very revealing: "I realised I could either go mad, join the Bin Ladenists, or step out of the religion."

This fanatical form of Islam was, she realised, around her in the Netherlands. On the night of September 11, a small group of Muslim men took to the streets to celebrate the massacre. The country's domestic violence shelters were disproportionately crammed with Muslim women fleeing male terror. Forced marriages and "honour killings" continued at a startling rate in Dutch cities. But she found that many otherwise good people were reluctant to speak out against this abuse of women and gay people within immigrant communities.

The Netherlands had a policy called "emancipation within your own circle", and Ayaan saw this as a betrayal. Multiculturalism, she believed, was "elevating cultures full of bigotry and hatred towards women to the stature of respectable alternative ways of life. I wanted Muslim women to be aware of just how bad, and unacceptable, their suffering was. I wanted to help them develop the vocabulary of resistance."

She took the great English feminist Mary Wollstonecraft as her lodestar, and began to campaign for the state to log the rate of "honour" killings, because nobody was even bothering to count. This led to the centre-right Liberal Party asking her to run to be a member of parliament.

She accepted, and got one of the highest personal votes in the country. This in turn led her into the path of Theo van Gogh – and to his slaughter. After that, Ayaan was placed under full-time surveillance by security guards and was barely permitted to leave her house.

****

At this point, two Ayaans were born, with clashing and contradictory views on Islam. Sitting here now, I can feel their presence; I can hear them alternate in her mind. I call the first "revolutionary Ayaan", and this Ayaan says about September 11: "This was not just Islam, this was the core of Islam. Mohammed Atta believed he was giving his life for Allah. This is beyond Osama bin Laden, it is based in the basic roots of Islam."

Without pausing, she continues: "You have to ask – is it a fact that the Prophet Mohamed conquered lands using the sword? Is it a fact that Muslims are commanded to commit jihad? Yes it is."

She has no time for what she sees as the ignorant, woolly Islam-is-peace message of Western liberals, insisting: "I see no difference between Islam and Islamism. Islam is defined as submission to the will of Allah, as it is described in the Koran. Islamism is just Islam in its most pure form. Sayyid Qutb didn't invent anything, he just quoted the sayings of Mohamed."

Revolutionary Ayaan believes that the religion cannot be reformed or changed, only defeated. The millions upon millions of Muslims who are not violent – "the wonderful, decent, law-abiding people" – simply do not really follow Islam. They ignore it, or they live uncomfortably with the explosive "cognitive dissonance" of simultaneously supporting human decency and the demands of Islam.

She lists the awkward truths about the Prophet Mohamed. "All Muslims believe in following his example, but many of the things he did are crimes. When he was in his fifties, he had sex with a nine-year-old girl. By our standards, he was a pervert. He ordered the killing of Jews and homosexuals and apostates, and the beating of women." That is why she concludes that "the war on terror is a war on Islam", and "Islam is the new fascism".

But then there is "reformist Ayaan". This Ayaan says the opposite: that internal reform within Islam is both possible and necessary. She insists: "It's wrong to treat Muslims as if they will never find their John Stuart Mill. Christianity and Judaism show that people can be very dogmatic and then open up. There is a minority [within Islam] like [the reformists] Irshad Manji and Tawfiq Hamid who want to remain in the faith and reform it.

"Can you be a Muslim and respect the separation of church and state? I hope a large enough number of Muslims will agree you can, and they will find a way to keep the spiritual elements that comfort them and live in a secular society."

Ayaan's life story is strewn with Muslims who rejected Bin Ladenist fanaticism. Her father, for example, was revolted by the Wahabbism he witnessed in Saudi Arabia, and told her: "This is not Islam – this is Saudis perverting Islam." She hesitates when I ask her about this fracture line in her thinking; I can almost touch the cognitive dissonance.

Then "reformist Ayaan" says: "Well, my father was trying to combine the commandments in the Koran with his conscience. He has reached a level of civilisation because he's living in the 21st century, but he was also trying to follow a religion founded in the seventh century. So on the one hand he thinks you should accept that the content of the Koran is the true word of God, and on the other hand he is a decent person. He tried to move on by saying that we should only convert non-Muslims by example, not by violence, and [by saying] that only the Prophet Mohamed can call for a jihad." But then "revolutionary Ayaan" adds: "That's not what the Koran says. It says you can never change the faith."

Is there is a danger that the language of "revolutionary Ayaan" is undercutting the very people "reformist Ayaan" wants to encourage? Does she worry that by calling all Islam "fascism" she might encourage the hard right, who want to deny women like her the chance even to come to Europe as refugees?

"I do," she says. "But the group of Europeans, white Europeans, who want to stop immigration altogether, and who reject Muslims, today in 2007, is not that large. But they could become larger if European governments continue the policy of accommodating and appeasing fascist demands made by radical Muslims. They need to oppose fascist demands by Muslims, and the fascist demands by far-right white groups. I think that if there is equal treatment on both sides, the traditional populations of Europe will say that it's fair play."

As we discuss this, I realise there is something odd about this conversation. It is all so disconcertingly normal. Ayaan is speaking in a level voice, at a level volume. If you didn't speak English and you saw us talking, you could assume that we were discussing bus timetables, or the weather. It's not that she seems passionless – not at all – but that her personality seems to be coiled up within her, and I am only seeing the carefully considered tip of it. When she describes the people who want to hack her body to pieces, it is in paragraphs that feel prepacked. Perhaps it is all she can bear to show.

And so we continue. She looks at me politely and says that Europe needs to be more confident about standing up to Islamic fundamentalism. "When we come here as immigrants, we know it will be different to where we come from. It's a choice to come, and we can always choose to leave. If we do not want to adopt European values, we should expect to be criticised."

For example, she says, the veil she used to wear is "a political statement, it's not just a religious statement. It says: I'm different from you and I reject what you stand for." She stresses that she doesn't want to ban it, just to see it challenged. "I'm opposed to banning of political expression, but I'm very much a proponent of competing political expression.

"The message of liberals is so much better, so much stronger, that you don't have to resort to banning. You can wear whatever it is that you want, you can give out whatever message that you want to give out – but you have to understand that if that message is rejected, then you can't call people Islamophobic and expect to be taken seriously. If you choose to wear a veil, people might ridicule and oppose you. That's their right, too."

****

She speaks with such eloquent intensity because she is arguing against another, younger version of herself. The Ayaan of 2007 is attacking the Ayaan of 1987 – who is damning her right back. If there is a clash of civilisations, it is happening within her. It's hard to remember, as we sit here, that there are tens of thousands of people who want to prematurely bring this fizzing debate inside Ayaan's head to an end – with a bullet.

She fell in love with Holland because of its tradition of unabashed free speech, but it seems the country's politicians have judged that she took free speech too far for them. Last year, the Dutch government began to reinvestigate the lies in her original asylum claim. Ever since she entered public life she had been totally candid about this: she exaggerated the degree of state persecution she faced because being abused by your family isn't enough to be granted refugee status. Now the government was twitchy about the rows she was stirring up – so they suddenly decided to strip her of her seat in parliament. Amid efforts to revoke her Dutch citizenship as well, she fled to Washington and a job with a conservative think-tank.

Her alignment with the American right doesn't seem like an easy fit. She is a militant defender of atheism, feminism and gay rights – all forces they have demonised for decades. She is an illegal immigrant, their ultimate hate figure. But, as our interview goes on, I realise she has depressingly begun to adopt some of their ideas. She wants to abolish the minimum wage. She no longer calls for the closing of all faith schools, but simply Muslim ones, because "they are the only ones that do not respect the division between secular and divine law".

She has even begun to touch on the American hard right's preposterous predictions that Muslims are "outbreeding" the continent's traditional populations and will impose sharia law "within decades". When I challenge her on this, she says that "experts" say it is true.

Then, this month, the Dutch government went further and stripped away her security protection, saying she should pay for it herself. The US government will not pick up the tab – the only mechanism they have for protecting private citizens full-time is the Witness Protection Program, which isn't appropriate.

"Only 11 members out of the 150 MPs voted to keep my security detail," she says. "So it's an overwhelming decision, and when I saw that I did feel betrayed. It's not only a betrayal of me, it's a betrayal of the idea of free expression.

"I think they believe that supposedly provoking Muslims will only make them more angry and hostile. The four large cities in Holland have now got very large Muslim populations, and that number is increasing – the estimate is that they're about 40 per cent. With that kind of electoral power [they think] it's best not to provoke them." Even if that means sacrificing basic Dutch values? "Yes."

She is revolted by the people who claim that it is she, Ayaan, who has "sold out" Muslims. "Tell me, is freedom only for white people?" she has written. "Is it self-love to adhere to my ancestors' traditions and mutilate my daughters? To agree to be humiliated and powerless? When I came to a new culture, where I saw for the first time that human relations could be different, would it have been self-love to see that as a foreign cult, which Muslims are forbidden to practise?"

So here she is, with the last sliver of protection she can afford standing between her and the people determined to murder her, still speaking, still fighting. Her family have said that they will never speak to her again. She knows she can never return to the country where she was born. Is she frightened? She answers quickly, as if reciting a reassuring script. "I know that is what these terrorists want me to be," she says. "So I try not to be scared." Then she pauses, and looks down. "But sometimes. Yes."

She looks up again. "But I am lucky. There are so many crossroads where my life could have become so much worse. If I had stayed in Kenya with the [jihadist] prayer group, if I had entered into the marriage my father wanted... I could have lived like my mother." She nods with confidence. "How many girls born in Digfeer Hospital in Mogadishu in November 1969 are even alive today? And how many have a real voice?"

Ayaan Hirsi Ali was in London to address the Centre for Social Cohesion