Mystery and romance cloak the Tuaregs, the blue-robed Sahara Desert nomads and marauders who have long been the subject of exotic adventure yarns and Hollywood movies.

But there is nothing fictional about the Tuareg rebels who have now conquered Timbuktu, also part of the colourful Indiana Jones-style lore of the Sahara, planting their yellow, green, red and black flag in the fabled city to declare an independent breakaway state and trigger an international crisis that is causing statesmen and diplomats huge alarm.

In just a few days the Tuaregs of the National Movement for the Liberation of Azawad (MNLA) have swept across a 300,000 square mile swathe of territory, threatening the continued existence of the state of Mali which has been one of the West's lodestars for the future of healthy democracy in Africa.

The rebels are formidable fighters, says Professor Jeremy Keenan of London University's School of Oriental and African Studies. Fiercely independent, the Tuaregs regard themselves as "lords of the desert" and were the main opponents of French troops during the colonial era. "They probably would have given any army a hammering," says Keenan. "The Malian army is pretty useless at the best of times, and they had already beaten a strategic retreat [before the Tuaregs' recent sweep through the north]."

As the US-trained Mali armed forces fell into disarray, a mutiny among junior officers two weeks ago ousted the country's elected president, Amadou Toumani Toure, after two decades of democratic rule. The mutineers — led by Captain Amadou Haya Sanogo, who received extensive training in the US between 2004 and 2010 — said they were angered that President Toure had failed to provide them with the weapons and strong leadership necessary to crush the Tuareg rebellion. But the mutiny further undermined the government's defences in the north, and town after town rapidly fell to the rebels.

Sanogo, under pressure from other West African states worried by the ripple effects throughout the region of a successful Tuareg secession, announced that he intends ceding power to the speaker of the Mali National Assembly as interim president pending new democratic elections. But the speaker, Dioncounda Traore, fled Mali after the military coup and there is no timetable for the handover. The announcement did not say what future role the military junta will play.

The rapid developments in the north have left the West and Africa's security establishments with many problems. The MNLA Tuaregs, who have declared an independent and secular Azawad state in northern Mali while renouncing claims on the rest of the country, entered the battle in a marriage of convenience with a powerful offshoot of al-Qaeda that seeks the conquest of all Mali.

The Tuaregs believe little can stop them now from establishing their Azawad state. Although official recognition will be difficult to achieve, Gilles Yabi, a West Africa specialist with the Brussels-based International Crisis Group, says: "They really believe that their Azawad state can be viable, and we must remember that, in Africa, the recent successful and recognised secessions of South Sudan and Eritrea are in everyone's consciousness."

However, Western and African leaders worry that the secession virus could spread throughout the Sahel region, where the Sahara Desert meets more southerly savannahs and forests, and northern Moslems abut southerly Christian and animist societies.

Mali's ambassador to the UN, Oumar Daou, said his country is in crisis. "The people are divided," he said. "Our country is threatened with partition, northern Mali is occupied by Tuareg rebels and Salafists [Islamic militants], and hundreds of thousands of refugees and IDPs [internally displaced persons] are currently living in unimaginable conditions.

"How is it that a country that was known and recognised as a benchmark, a country in which the democratic model had taken root, is finding itself before the international community needing its help?"

In truth, it is hard to overstate the apocalyptic mess that Mali has become and impossible to predict the immediate course of events. "The fallout from unresolved colonial era issues may cause further chaos and instability throughout the region," says Alain Chouet, former head of the DGSE, the French intelligence service. "Secessionist tendencies everywhere may now accelerate."

The Tuaregs' "ally" in the conquest of Timbuktu and the entire north is the Islamist Ansar ud-Din (Defenders of the Faith) movement, led by former Tuareg nationalist rebel leader, Iyad Ag Ghali. Ansar ud-Din is closely allied with al-Qaeda's Algeria-origin north Africa branch, al-Qaeda in the Islamic Maghreb (AQIM). But Ag Ghali insists that Ansar ud-Din does not share the MNLA's goal of an independent Azawad state: it wants to introduce sharia law to the whole country. An estimated 95% of Malians are Muslems, but many, including most Tuaregs, are loyal to the relatively liberal Sufi sect.

The Tuaregs' demand for self-determination is centuries-old. It precedes the establishment by French colonialists more than 50 years ago of the independent state of Mali, into which the Tuareg were incorporated against their will. Before the current uprising, there had been numerous Tuareg attempts to achieve independence punctuated by fragile peace deals with Bamako, the Mali capital in the southern black African part of the country.

Iyad Ag Ghali was a charismatic leader of several of the Tuareg nationalist uprisings. A master of desert conditions and a camel racer in his youth, he is an acknowledged Tuareg history expert and is revered by his own clan, the Ifora, as the "lion of the desert". Angered by the "suffering" of the Tuareg, marginalised by Bamako, he first took up arms in 1990 and spearheaded an attack on a military camp which kick-started a five-year Tuareg rebellion.

Then in the early 2000s, when AQIM took shelter from Algeria's security forces in northern Mali, foreign governments asked him to negotiate the release of several foreign hostages taken by various Sahelian rebel and criminal groups. It was during this time, his followers say, that he visited Pakistan, discovered the "true faith" and became radicalised.

In January 2012, when the MNLA began the latest offensive for Tuareg independence, Ag Ghali resurfaced as the leader of Ansar ud-Din. Early on, after the MNLA had seized the desert town of Tessalit, Ag Ghali told the nationalist leaders: "I am not for independence. I want sharia for my people." Further serious fractures in the MNLA-Ansar ud-Din relationship began appearing when the rebels took the town of Kidal, regarded by Ag Ghali as his own "home" territory.

In recent days the most profound problems have arisen in Timbuktu where, according to numerous reports, Ansar ud-Din and Ag Ghali, flanked by the top three Algerian leaders of AQIM, have driven the MNLA nationalist Tuareg forces to the outskirts of the city and begun implementing sharia law.

Referring to "uncultivated Westerners", Ag Ghali preached on the newly captured Timbuktu Radio: "All who are not on the path of Allah are infidels. Our struggle is reform. Our enemies are miscreants and polytheists. We must fight all who oppose the development of Islam. We must eliminate them. It is a holy war we must lead."

Increasingly the black al-Qaeda flag is displacing the rainbow flag of the Tuareg nationalists and speculation is rife that an internal war between the MNLA and Ansar ud-Din for control of the north will soon begin.

Among the many unanswered questions is what all this will eventually mean for the Tuareg and for historic Timbuktu.

The Tuareg are a Berber, nomadic, non-Arab, non-black African group sometimes called the Blue People because the indigo used in their traditional flowing robes and turbans dyes their light-coloured skins dark blue. They prefer to call themselves the Kel Tamasheq – or "speakers of Tamasheq", their language which has its own alphabet. They see themselves historically as discriminated against racially by both Arabs and black Africans. Back into the sands of time they have lived in a vast Sahara and Sahel region they have always called Azawad, encompassing mainly what is now northern Mali and northern Niger, but also southern Algeria, south-west Libya and northern Burkina Faso.

In post-colonial Mali, where they comprise about 1.5 million of the 15 million population, they say they have been neglected by the distant government in Bamako as well as being discriminated against because of their light-coloured skin.

Tuaregs founded Timbuktu, at the confluence of several trade routes on the southern edge of the Sahara and the far northern bend of the Niger River, in the eleventh century AD.

The potential fate of the city under the possible rule of Iyad Ag Ghali is of intense concern to the international cultural community. Its spectacular mud mosques and mausoleums rise from the sand like organic parts of the desert. Irina Bokova, director-general of Unesco, called on all sides in the conflict to safeguard the city's "outstanding architectural wonders", designated World Heritage Sites.

But in hard-headed Western capitals, strategists watching the situation, the new rules of the game are unclear, and Britain has withdrawn its staff from its embassy in Bamako. The US is stunned by the realisation that a decade of special forces training for the Mali armed forces, intelligence and development cooperation from Washington, democratisation programmes and counter-terrorism programmes have, at best, failed to prevent the new chaos in the desert and, at worst, helped to sow its seeds.

The Tuareg say they have been neglected by the distant government as well as being discriminated against because of their light-coloured skin

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