AMISOM troops capture territory from insurgents in MogadishuSomalia’s Harakat al-Shabaab al-Mujahedeen joined al-Qaeda in February 2012. News of the new union prompted celebrations in southern and central Somalia, areas long controlled by al-Shabaab.

Since the announcement, the frequency of attacks against Somali government and foreign peacekeepers has dramatically increased. Somali Islamists regard al-Qaeda as the vanguard of Islamic movements worldwide. They also attribute the withdrawal of U.S. forces from Iraq and their pending departure from Afghanistan to al-Qaeda’s competence. Thus, al-Shabaab hopes this new alliance will help rid Somalia of foreign influence, including foreign forces, and pave the way for the eventual establishment of Islamic law.

Al-Qaeda’s union with al-Shabaab threatens both the Horn of Africa—Somalia, Ethiopia, Sudan, Eritrea and Djibouti—and East Africa, which includes Kenya, Uganda and Tanzania. Although al-Qaeda has suffered massive degradation since Osama bin Laden’s death, its footprint is expanding in Africa. It has already established an ideological and operational presence in three areas on the continent—the Maghreb, the Sahel and West Africa. A large Muslim population, an especially large youth population and porous borders make Africa ripe for ideological extremism and terrorism. Without significant international investment to fight poverty, corruption and poor governance, the influence of al-Qaeda and its associated groups will spread to other parts of Africa in the coming decade.

The Rise of a Union

The Union of Islamic Courts (UIC), a coalition of Islamist groups in Somalia, occupied much of southern and central Somalia by mid–2006. When the UIC broke up later that year, its military wing—the hardline al-Shabaab—eclipsed its political wing. After imposing strict sharia law in Somalia, al-Shabaab’s religious police enforced a Taliban-style regime: whipping women wearing bras, stoning to death accused adulterers, carrying out amputations for robbery, punishing through floggings and beheadings, and instilling fear through kidnappings, shootings and targeted assassinations.

But al-Shabaab’s hold on the country has weakened over the past five years. As a result, its leadership has gravitated closer to al-Qaeda. Last month’s unity declaration is best understood as the culmination of this process. Al-Shabaab leader Sheikh Mohamed Mukhtar Abdirahman, or "Abu Zubeyr," pledged allegiance to al-Qaeda leader Dr. Ayman al-Zawahiri in a video released by al-Qaeda's media arm. Posted on jihadist forums, the video featured an audio speech from Zubeyr and footage of an address by Zawahiri. Zubeyr informed Zawahiri that al-Shabaab enjoys success and "great fortune" in its jihad in Somalia and congratulated Zawahiri on the "defeat" of U.S.-led forces in Afghanistan and Iraq. Zawahiri seemed optimistic: "Today, I have glad tidings for the Muslim Ummah that will please the believers and disturb the disbelievers, which is the joining of the Shabaab al-Mujahideen Movement in Somalia to Qaedat al-Jihad, to support the jihadi unity against the Zio-Crusader campaign and their assistants amongst the treacherous agent rulers."

A History of Cooperation

Relations between al-Qaeda and Somali Islamists date back to the early 1990s, when al-Qaeda made inroads to Somalia following the collapse of the Somali state after a terrible civil war and famine. Al-Qaeda set up a base of operations similar to that in Afghanistan, establishing training camps and conducting a few attacks to spark the imagination of Somali Islamists. Members of al-Shabaab were instructed on terrorist tactics—suicide attacks, roadside bombs, assassinations, poisons—and on developing platforms and disseminating propaganda to radicalize and recruit other Somalis. This cost-effective strategy allowed al-Qaeda to impart its methodology of “martyrdom operations” and its ideology of global jihad to al-Shabaab, effectively sowing the seeds for collaboration between the two groups.

But despite its training operations and involvement in a number of attacks, al-Qaeda failed to gain significant traction in Somalia. In general, Somali leaders did not like al-Qaeda’s strategy of perpetual war. Tribal loyalty, Sufi philosophy and fighting between the factions created an unstable environment for al-Qaeda to establish a permanent base of operations. But all this changed with the Ethiopian intervention in 2006.

Foreign Intervention, Islamist Collaboration

In response to the intervention of U.S.-backed Ethiopian forces (largely Christians) in July 2006, Somali Islamists looked to al-Qaeda for support. Zawahiri responded, calling upon Muslims everywhere to participate in the jihad and provide Somali Muslims with men, experience, money and advice to defeat the Ethiopian forces, whom he referred to as the “slaves of America.” He encouraged members of al-Shabaab to “use ambushes and mines, and raids and suicidal attacks until you rend and eat your prey as the lion does with his prey.” In April 2009, Bin Laden himself framed the conflict in Somalia as a war between Islam and the international crusade.

Determined to break the al-Qaeda–al-Shabaab link, the United States targeted both al-Qaeda leaders and their facilitators in al-Shabaab. Beginning in January 2007, Washington mounted multiple operations, including air strikes, against al-Qaeda operatives and training camps in Somalia. They met with some success, in November 2007 killing Abu Talha al-Sudani, a Hezbollah-trained al-Qaeda leader who had planned attacks in Djibouti and Kenya; and in 2008 taking down al-Shabaab’s military commander. Subsequent U.S. naval strikes targeted Abu Talha’s successor, Saleh Ali Saleh Nabhan. After escaping several raids, Nabhan was killed south of Mogadishu in September 2009 by U.S. Navy SEALs in a helicopter raid staged from a ship. The mission, known as Operation Celestial Balance, presaged the May 2011 killing of Bin Laden—including the fact that the SEALs took his DNA, then disposed of Nabhan’s body at sea.

In 2011, Somali forces killed Nabhan’s successor, Fazul Abdullah Mohammed, and his personal assistant, who was both recruiter and financier of the July 2010 double suicide bombing in Kampala that killed seventy-four and injured seventy. But there is still much work to be done; al-Qaeda’s patron Hassan Dahir Aweys, the spiritual leader of al-Shabaab, is still active. To create space for the Transitional Federal Government and the African peacekeepers to stabilize Somalia, the United States must continue to train local forces and hit high-value targets.

What’s Next?

Given the severe challenges confronting al-Qaeda in Pakistan and Afghanistan as well as in the Levant, the Arabian Peninsula and the Maghreb, news of the al-Shabaab–al-Qaeda union was celebrated by the global jihadi community. The union is not a superficial one; it is the formalization of a relationship of cooperation and collaboration spanning two decades. Al-Shabaab will benefit greatly from al-Qaeda’s support, both in terms of finances and in terms of recruits. As the vanguard of the Muslim militant groups, al-Qaeda leaders have called upon their supporters and sympathizers to support al-Shabaab against the Somali military and the African Union peacekeepers. Al-Qaeda, weakened on many fronts, will benefit from making Somalia a key hub for operations in Africa. The union with al-Shabaab provides al-Qaeda the opportunity to expand into a promising new frontier.

The international community should contain the threat from Somalia by supporting the Transitional Federal Government of Somalia and peacekeeping forces. As part of the African Union Mission in Somalia, soldiers from Djibouti, Uganda, Burundi and Kenya will replace Ethiopian forces planning to pull out of Somalia shortly. If these forces fail to confront the new al-Shabaab-al-Qaeda alliance, the consequences for Somalia, Africa and the global fight against terrorism will be dire.

Professor Rohan Gunaratna is head of the International Centre for Political Violence and Terrorism Research in Singapore, author of Inside Al-Qaeda (Columbia University, New York, 2002) and lead author of Pakistan: Ground Zero Terrorism (Reaktion, London, 2011).