The east African coast — from Kismayo in southern Somalia down to Beira in Mozambique — is one of the most beautiful places on earth. Palm trees wave on glittering beaches, lapped by waves full of parrot fish and lobster. Deeper inland there’s dark green, virgin bush, studded with frangipani, spice plants and outcrops of rock. Offshore, islands such as Zanzibar, the Comoros and Lamu are — at least on the surface — paradisal idylls.

They seem like the kind of place you might go on holiday. Many tourists do go to them, especially to Zanzibar and to Kenya’s Indian Ocean resorts, Mombasa and Malindi. If anything, the danger seems to be that of coastlines everywhere: too many hotels. But what if, as happened to a friend of mine, you saw a dhow pass by with a flag bearing the image of Osama Bin Laden? You’d be seeing the key to the hidden world of this area, one I’ve become fascinated by as a novelist and journalist.

Most of my early life was spent in central Africa — including Uganda, where I wrote The Last King of Scotland — but latterly I’ve tended more to these alluring destinations on the coast. Not just for pleasure: this coastline has over the past decade become an Al-Qaeda haven. The Somali littoral, most acutely, has been a focus for terrorist activity.

In this context came last week’s US airstrikes, led by AC-130 gunships, against targets in southern Somalia. They took place in conjunction with the Ethiopian army and forces of Somalia’s transitional government pushing hardline Islamic Courts fighters southeast to a corner between the sea and the Kenya border: in particular, to Badmadow Island. It’s one of a group of six rocky, forested islands in a coastal area known as Ras Kamboni.

Ras means “cape” in Swahili/Arabic. It is a common prefix in these parts. All up and down the coast there are similar locations off and onshore. Remote, thinly populated, often densely thicketed, with high-frequency radio the only reliable form of communication, they are the perfect nest not just for Al-Qaeda, but also for drug runners and pirates.

International criminal gangs have penetrated the region, turning the shores of Somalia, Tanzania, Kenya and Mozambique into transit points for drugs such as heroin, cocaine, mandrax and hashish. These drugs, originating mostly from the Asian continent, are destined for southern Africa, Europe and North America. The Chinese, who now have a large and not always legitimate interest in Africa, have a big hand in this seaborne trade.

At the same time, piracy is on the increase. In 2005 a luxury cruise ship with 22 British tourists aboard survived an attack by Somali pirates armed with rocket-propelled grenades, fending them off with the aid of a “sonic blaster” that emitted high-powered air vibrations.

The area has long been an enclave for pirates, with Captain Kidd’s travels having taken him out to the Comoros and down to Madagascar in the 1690s. Madagascar was supposedly the site of “Libertatia”, a semi-mythical free colony run by pirates for about 25 years from 1600. Today, there are more than 20 attacks on international shipping off the east African coast every year.

It is, forbiddingly, in this lawless region that Al-Qaeda has sequestered itself (Somalia has had no recognised government since 1991). But the law may have finally caught up with it. With a bunch of Al-Qaeda’s key leaders under attack — although early reports that Fazul Abdullah Mohammed, one of the organisation’s big three in Africa, had been killed turned out to be premature, the organisation has been weakened. Mohammed’s wife and three children were arrested in the Kenyan coastal town of Kiunga on Monday. The two other principal Al-Qaeda east African leaders being sought are Saleh ali Saleh Nabhan and Abu Taha al-Sudan.

I based a character on Mohammed in my novel Zanzibar. The writing of that book was my introduction to the link between Al-Qaeda and this coastline. It took me completely by surprise. The year was 1998, long before the name Osama Bin Laden was on everybody’s lips. I was on an unrelated journalistic assignment on Zanzibar, off the coast of Tanzania, when Al-Qaeda detonated two vehicle bombs at the US embassies in Nairobi and Dar-es-Salaam, the Tanzanian capital: 224 people were killed.

I didn’t know it was the beginning of the war on terror, but I knew it was something important. My immediate suspicion that the bombers had used the porous, mysterious east African coast as a springboard for the attacks proved correct. I had just finished my novel when, three years later, 9/11 happened.

Mohammed is a Comorian with a $5m (£2.55m) bounty on his head. A skilled bomb-builder and master of disguise, he was executive controller for the embassy bombings. One of the other bombers, Khalfan Khamis Mohamed, was from Pemba, an island off Zanzibar; a third, Mohammed Odeh, ran a fishing boat out of Mombasa.

Captured by the US, Odeh gave testimony in his 2001 trial as to just how deep Al-Qaeda penetrated this coastline during the early 1990s, when America led a United Nations force into Somalia in an effort to fight famine. The mission saw clashes between UN forces and Somali warlords, including the humiliating Black Hawk Down battle of 1993 that killed 18 US soldiers. Odeh told how he and Saleh remained in Somalia aiding clan leader Mohammed Farah Aideed for a full year, and “considered the humiliation of US troops a major victory”.