Smuggling, banditry, and political unrest have long plagued large swathes of the Sahara, but in recent years two new destabilizing forces have entered the scene—terrorism and drug cartels.

For several years, the group now known as Al Qaeda in the Maghreb (AQIM) has launched attacks in Algeria from remote bases inside Algeria and across the border in the northern desert of Mali. More recently, they have begun staging attacks in Mali, Mauritania, and Niger, while steadily courting support from among Arabic-speaking, nomadic clans sprinkled throughout in the desert.

To fund their activities, AQIM has kidnapped Westerners (47 since 2003), netting an estimated $100 million in ransoms. Their coffers have been further bolstered by protection money from South American drug cartels, which smuggle cocaine through the desert to the Mediterranean coast and on to Europe where demand for the drug continues to grow. According to Interpol, some $2.2 billion worth of cocaine is funneled annually through the region.

At the center of this tumult are the Tuareg, the turbaned nomads who have inhabited this part of the Sahara for centuries. For much of the last three years, Tuareg groups in Mali and Niger waged violent rebellions against their respective governments, seeking greater voice in how their lands and resources are administered. Though a peace deal was brokered earlier this year, the conflict has left much of the region impoverished and awash in weapons and unemployed former fighters. Observers in the region worry that many of these young men could fall under the sway of AQIM and the cartels.

Since 2008 National Geographic staff writer Peter Gwin has traveled the region, living with Tuareg families, embedding with rebel bands, hitching rides with smugglers, and following nomad caravans to document the desert’s evolving social and political landscape.

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Peter Gwin has been a staff writer at National Geographic since 2003. He has reported on modern pirates in Southeast Asia, a Stone Age graveyard in the Sahara, early tyrannosaurs in Western...