The words may be fictional but, as we count down to Washington's second instalment in the real-life epic that is the the war on terror, an honest examination of what has brought the civilisations of Islam and the west to this critical pass is long overdue. For despite the seemingly unassailable sway of the clash of civilisations thesis - in some quarters more a desire than a forecast - there is hope and it lies in the fact that the differences are less intractable than the forces of darkness would have us believe.

Five years ago, the Iranian president Mohammed Khatami called for a "dialogue of civilisations" before a meeting of the UN. The speech was an encomium to liberty, articulating what progressive Islamists have been advocating for years as the key to peace: emancipation from despotism. The major obstacle to peace, goes the theory, is not terrorism or religious obscurantism but the enslavement of hundreds of millions of Muslims, who continue to be denied the fundamental right of being free to choose their own leaders and systems of government.

The warmongers have made sure the message has remained outside mainstream debate so they can forge ahead unimpeded. Using their agents and sympathisers in the mass media to blanket all Islamist politics as fundamentalist, and by excluding its fluid, nuanced discourse from the international conversation, they have rendered voiceless a full quarter of humanity.

Because most Muslim politics is Islamist the political and media blackout has meant the grievances of subject Muslim populations have failed to reach their free counterparts in the west. How many on the Clapham omnibus know that France actively supported the Algerian government's annulment of elections that Islamists were poised to win in 1992, plunging the country into a savage civil war? Or that in Egypt, whose single-party regime qualifies in Washington as the second most-favoured tyranny after Israel, religious parties are banned, as they are in Turkey, and political dissidents tortured? Or that since the "accession" of the Palestinian National Authority, Palestinian newspapers critical of Arafat have been banned and their editors spirited away to jail in the middle of the night to be flogged back into line? Or that in Jordan political activity in mosques is outlawed?

The governments of the west decree that liberty is not a fundamental right for Muslims; it is a privilege to be extended in proportion to the degree to which they conform to their prescriptions, especially that of secularisation. The war on terror is part of a campaign to wrench Muslim societies from their religious roots, a phenomenon that has best been explained by Rachid Ghannouchi, a Tunisian Islamist ideologue now exiled in Britain.

For Ghannouchi the war against Islam began with Napoleon's invasion of Egypt in 1798 and continued through the era of colonialism when opposition was monopolised by a secularised elite that eventually supplanted the colonial regimes. However, instead of actualising the Koranic principle of shura (community consultation) to build democratic polities in which the will of the majority is recognised, they set about doing violence to the faith in the mistaken belief that progress and development could only be achieved by aping the west.

But there was a crucial difference in the secularism enshrined in western polities and the aggressive totalitarian variant imposed in the Muslim world. While the former merely separated the religious from the mundane leaving some space for religion as in Britain, Arab pseudo-secularism sought to take control of the institutions and symbols of Islam. Resistance was met with state repression and violence.

Ghannouchi lists how Tunisia's post-independence autocrat Habib Borguiba tried to sever ties with its Islamic past, abrogating sharia law, removing religion from the curriculum of Zaytuna University before closing it down altogether, and nationalising mosques and the awqaf (relig-ious endowments that gave religious institutions such as schools and charities indepen-dence). He also issued a fiat ordering state employees to break the Ramadan fast and restricted the number of pilgrims performing the Hajj. For Tunisia you could substitute almost every other Arab nation-state.

Pseudo-secularism was necessary to remould the Muslim mind into accepting the western separation of church and state. There was no theoretical basis in Islam to render the political sphere unto Caesar. To the contrary - Muslims had to be forced by the state to adopt it. Anybody who believes the age of desacralisation has passed need only look at the demands being made by the US on Pakistan's General Musharraf and Indonesia's President Sukarnoputri to "reform" the Islamic schooling system, or madrasa, as a check against "extremism".

That secularism has been placed ahead of liberty is, says Ghannouchi, the result of malevolence but also a mis-conception in the western mind that sees in all religion the European struggle against a church that in the Middle Ages opposed the ability of reason to explain the universe and to organise life.

Since Islam has no inherent objection to reason - a facet demonstrated by the wealth of scientific knowledge it bequeathed to the Renaissance - it is inappropriate to view it through this lens. What we did have in the Muslim world was no end of autocracy. While the ulema (scholars who interpret the religion) shielded religious institutions from the state's will to power by anchoring them in civil society, they failed to develop a theory of governance rooted in the democratic practice of the early community in the city state centred on Medina.

Like many Islamists, Ghannouchi insists on the compatibility of democracy with Islam. Controversially for some Islamists, he advocates British-style secular democracy as a step to a democracy rooted in the divine law, since any type of democracy is better than the despotism that is Muslims' lot today.

"The conflict is not a religious one," he writes. "Nor is it even a conflict between religion and the western concept of secularism. It is a political conflict between the oppressor and the oppressed. It is about legitimacy and whom it belongs to. It is about the nature of government, the choice between autocracy and democracy."

Last week Jack Straw took the war on Iraq to the world's most populous Muslim nation, Indonesia, claiming that Saddam posed as great a threat to Muslims as he did to the west. Nice try, mate. Autocratic Saddam poses the same threat to Muslims as the "autocratising" west.

· Rachid Ghannouchi - A Democrat within Islamism by Azzam S Tamimi is published by Oxford University Press.