By mid-2008, insurgent forces controlled most of southern and central Somalia as well as most of Mogadishu. The TFG-Ethiopian alliance held only a few blocks of the capital, including the port, airport, and presidential palace. The support base for extremists was much larger and more radical than it had been before the Ethiopian invasion, and terrorist threats were far more serious. Even Western diplomats recognized that Islamists had to be included in negotiations for any future government that had a chance of success. In June, moderates in the TFG and the Alliance for the Re-liberation of Somalia (ARS), an opposition coalition composed of both Islamist and secular groups, met in Djibouti to negotiate terms for peace. Al-Shabaab, which controlled much of southern Somalia, opposed collaboration with the secular parties and refused to participate.
The ensuing Djibouti Agreement, backed by the UN, the AU, the EU, and the United States, resulted in a number of changes on the ground. In January 2009, the Somali parliament was enlarged to include moderate Islamists, representatives of citizens’ groups, and Somalis from the diaspora. The parliament elected a new president, selecting Sheikh Sharif Sheikh Ahmed, an ARS leader and Sufi moderate who had led the ICU executive council before the foreign invasion. By the end of the month, Ethiopia had withdrawn its troops from Somalia. In April the new parliament voted to make Islamic law the basis of the Somali legal system. The insurgents’ rallying points were severely weakened. The foreign occupier had withdrawn, an Islamist had been elected president, and Islamic law was being implemented throughout the country. A number of Muslim factions that had opposed the TFG agreed to lay down arms. Ahlu Sunnah Wal Jama’a (Followers of the Prophetic Way and Consensus), an alliance of Sufi militias backed by local clans, agreed to resist al-Shabaab and to back the Sheikh Sharif government. However, other factions persisted. In February 2009, an alliance of Muslim insurgent organizations that had rejected the Djibouti Agreement established Hizbul Islam (Islamic Party) under the leadership of Sheikh Hassan Dahir Aweys, erstwhile ICU consultative council leader, onetime Sheikh Sharif ally, and subsequent ally of al-Shabaab. In May, Hizbul Islam and al-Shabaab conducted a joint operation against TFG forces in Mogadishu, where AMISOM forces saved the government from destruction.
Despite the reforms mandated by the Djibouti Agreement, the TFG remained weak and unpopular. It was corrupt, unrepresentative of the popular majority, and beholden to outsiders. Determined to retain a monopoly on power and resources, it refused to engage with local political and military forces that might threaten its position. It failed to build state institutions and relied on foreign backers to uphold its power. In the northwest (Somaliland) and the northeast (Puntland), autonomous regional governments exercised de facto authority without Mogadishu’s approval or support. Some TFG-allied militias, including Ahlu Sunnah Wal Jama’a, joined Ethiopian soldiers in targeting civilians and were roundly condemned by human rights organizations.
Although the departure of Ethiopian troops was widely applauded inside Somalia, the AMISOM force also generated intense hostility, even among those who opposed al-Shabaab. AMISOM’s heavy shelling of urban neighborhoods, like the Ethiopian attacks, had resulted in large numbers of civilian deaths. Many Somalis also chafed at the presence of thousands of troops from neighboring countries where the regimes in power were dominated by Christians and where Muslims faced repression and discrimination. Al-Shabaab played on these sentiments and characterized AMISOM as a Christian invading force. Nor was AMISOM particularly effective. Al-Shabaab retained a strong presence in Somalia, and on AMISOM’s watch it expanded its operations into neighboring countries. In July 2010, al-Shabaab engaged in its first cross-border operation, setting off coordinated bombs in Kampala, Uganda, that killed seventy-six people in retaliation for Uganda’s central role in AMISOM. Although AMISOM expelled al-Shabaab from Mogadishu in August 2011, the insurgent organization continued to control most of the country’s southern and central regions.
Al-Shabaab’s tenacity sparked a new episode of foreign military intervention in 2011. In October, some 2,000 Kenyan troops, followed by hundreds of Ethiopian troops in November, crossed Somalia’s southern border to attack al-Shabaab and establish a buffer between the two countries. The civilian death toll provoked animosity toward the Kenyan government, and al-Shabaab vowed to retaliate. Although Kenya claimed to be acting at the invitation of the TFG, the UN Security Council had tasked AMISOM with peacekeeping in Somalia. No other foreign entity was authorized to intervene militarily in Somali affairs. Nonetheless, the UN Security Council condoned Nairobi’s unilateral action, and in July 2012 AMISOM formally assumed authority over the Kenyan occupation force, giving it a veneer of legitimacy. Responding to the escalated international response and hoping to boost its image and fighting capacity, al-Shabaab formally merged with al-Qaeda in February 2012.
The year 2012 marked the end of the eight-year transitional government, but not an end to the Somali crisis. The new political dispensation—complete with constitution, parliament, and president—was once again the product of outside forces. It was mediated by the UN, backed by the international community, and disavowed by large segments of Somali civil society, which had had little input into the process. The new president, Hassan Sheikh Mohamud, was a moderate Islamist with links to the Islamic Courts Union and Somalia’s Muslim Brotherhood. He was also an educator and longtime civil society activist who had worked with the UN in various capacities. However, his ability to effect change was limited, and foreign troops continued to battle al-Shabaab on Somali soil.
In late September, Kenyan AMISOM soldiers, assisted by Somali government troops and militias, weakened al-Shabaab’s economic base when they gained control of the strategic southern port of Kismayo. A key transit point for foreign fighters, weapons, and supplies entering Somalia, and for the export of sugar, livestock, charcoal, and khat, the port hosted an illegal trade that generated hundreds of millions of dollars a year for al-Shabaab and its collaborators in the local Somali administration, as well as for the Kenya Defence Forces and Kenyan government. Although Somalia and Kenya officially sought an end to the turmoil, the enormous profits engendered by a lawless society served as an incentive for many to continue the conflict.
By 2012 al-Shabaab was diminished, but not defeated. As it lost territory and revenues, the organization changed tactics, focusing increasingly on unprotected soft targets, including government offices, schools, hotels, and restaurants. As it was ousted from towns and cities and pushed to Somalia’s southern border, al-Shabaab targeted rural populations in Kenya’s North Eastern Province. Distrusted and neglected by the Nairobi government, the predominantly Somali population of this area was especially vulnerable. While these killings provoked little international response, world attention was captured by al-Shabaab’s September 2013 attack on an exclusive Nairobi shopping mall that claimed the lives of sixty-seven people, including many foreign nationals. AMISOM forces, led by Kenyan soldiers, responded with an aerial offensive that killed some 300 al-Shabaab militants. In 2014, AMISOM forces were bolstered with more than 4,000 Ethiopian troops. Critics warned that the reengagement of the Ethiopian military would serve as a rallying cry for al-Shabaab.
Meanwhile, the United States escalated its low-intensity war against al-Shabaab operatives, deploying both private contractors and US Special Operations Forces, who trained and advised African partners, participated in raids, and interrogated prisoners. During 2014–16, US attacks killed Ahmed Abdi Godane, al-Shabaab’s leader since Ayro’s death in 2008; the organization’s intelligence chief; the official who purportedly planned the 2013 Nairobi mall attack; and some 150 militants in an al-Shabaab training camp. However, middle-level commanders quickly replaced assassinated leaders, and the insurgents continued to attack AMISOM and Somali troops, government officials, and civilians. The defection of a high-level al-Shabaab commander to the Islamic State in October 2015 and the formation of two new organizations, the Islamic State in Somalia and the Islamic State in Somalia, Kenya, Tanzania, and Uganda, resulted in even more brutality on the ground. Meanwhile, AMISOM forces were weakened. In 2016, the EU reduced its funding. The AU