Al-Shabaab has clearly declared war on the government of Kenya. But why? And why now?

Al-Shabaab’s origins and home base are in Somalia. Influenced by al Qaida, Al-Shabaab sought to partition Somalia into areas of control, from the coastal region which nurtured pirates to the south-eastern portion bordering Kenya. Al-Shabab and the Somali government have been fighting a bloody war for control of the capital of Mogadishu for some time.

Somalis are a clan-based people and are not particularly united. Governance in Somalia is steeped in rampant corruption, making the country fertile ground for terrorist infiltration. But natural disasters have played a role too — especially 2011’s great drought in the Horn of Africa, which saw tens of thousands die. Many Somalis fled the country into neighbouring Kenya, fleeing both famine and a rising tide of violence and coercion.

Many of those refugees landed in a refugee camp near the border called Dadaab, where over half a million Somalis live at a subsistence level. Some families living in the camp are now into their third generation there. Most can’t leave because they have nowhere to go. And Al-Shabaab operatives have turned the camp into a safe haven; Kenyan security officials treat it as a no-go zone.

In 2011, Kenyan troops joined AMISOM — a regional peacekeeping force formed under African Union auspices — in Somalia. The Kenyans moved into what had been Al-Shabaab strongholds in the south in an attempt to contain the terrorist army in Somalia and destroy it. Seen as occupiers, the Kenyan troops have not been welcomed by local Somalis — making them a target for attacks.

But this is not the real story. Kenya has long had a Muslim minority — about seven per cent of a population of forty-four million (rising to fifteen per cent on the coast) and growing quickly. Many of these Muslims are not Somali in origin and are based in what was Coast province near Mombasa, the descendants of Arab traders. Meanwhile, there’s a large community of Somalis who migrated — some legally, most not — to the Eastleigh district of Nairobi, Kenya’s capital.

What these two groups have in common is their marginalization from mainstream Kenyan society. Among them, male youth unemployment is high and education levels are spotty. So it’s not surprising that many are drawn to jihadist violence. Kenyan security forces discriminate against them and harass them. Criminality in the Coast region may be high (drugs, human smuggling, money laundering), but Kenya’s brutal treatment of its Muslim population fans the flames of Islamist violence and serves to recruit for Al-Shabaab.

Despite the vivid rhetoric deployed by Kenya’s President Uhuru Kenyatta, and the air strikes Kenya has directed against Al-Shabaab strongholds in Somalia, the threat isn’t going anywhere — because it’s rooted in Kenya itself. More inclusive policies that help Kenya’s Muslim minority integrate into the larger society would help, but they’d take time.

In the meantime, Al-Shabaab will continue to launch grisly attacks within Kenya, opposed only by security and intelligence services that are uncoordinated, under-equipped and indifferently led. More tragedy — for a nation that has suffered far more than its share.

David Collins is a former Canadian High Commissioner to Kenya, a fellow of the Canadian Defence and Foreign Affairs Institute, a director of the CDA Institute and an adviser to the Canadian Ditchley Foundation.