While the UN and the United States were preoccupied with the secular warlords, Somali Islamists were also building their base. Like many of its secular predecessors, al-Itihaad promoted irredentist claims with the goal of uniting ethnic Somalis from Ethiopia, Kenya, Djibouti, and So-malia in a single nation. However, in contrast to secular leaders, those in al-Itihaad envisioned Greater Somalia as an Islamic state. Perceiving opportunity in the chaos, al-Qaeda determined that Somalia was ripe for a jihadist insurgency that could serve as a launching pad for similar uprisings in Eritrea, Yemen, and the Muslim holy land of Saudi Arabia.
By late 1993, Sudan, Iran, and al-Qaeda were supplying al-Itihaad with money, weapons, military training, and personnel to counter US influ-ence in the region.
As the security situation deteriorated and Western aid organizations withdrew, Muslim charities supported by wealthy patrons in Saudi Ara-bia, the United Arab Emirates, and Kuwait filled the void. In a country with virtually no functioning infrastructure or social services, al-Itihaad provided assistance to the poor and established Qur’anic schools, Islamic courts, and militias to perform police duties. It invested in banking, telecommunications, export-import, and transportation, using business proceeds to finance social services and religious and political endeavors.
Through the application of shari’a (Islamic law), the Islamic courts pro-vided a justice system in a society buffeted by lawlessness and violence, where warlords and their gunmen raped, robbed, kidnapped, and killed at will. Desperate for law and order, a working economy, and basic social services, the Somali public generally supported al-Itihaad’s efforts, while Somali business owners endorsed the courts and financed their law en-forcement activities.
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Instability in Somalia precipitated a new crisis with Ethiopia. In 1994, al-Itihaad established a military presence near the borders with Kenya and Ethiopia and launched numerous attacks inside Ethiopia, especially in the Somali-inhabited regions. By 1996, Ethiopia was making regular incursions into Somalia to challenge al-Itihaad and build alliances with Somali warlords. In 2000, a group of Ethiopian-backed warlords formed the Somali Reconciliation and Restoration Council (SRRC), led by Ab-dullahi Yusuf Ahmed, who would become president of Somalia in 2004 as a member of the foreign-backed Transitional Federal Government (TFG), and by Hussein Mohammed Aidid, who had succeeded his fa-ther, Mohammed Farah Aidid, as head of the powerful USC militia.
Instability in Somalia also inspired new US concerns. US counterter-rorism experts warned that Somalia had become a haven for al-Qaeda—
including operatives responsible for bombing the US Embassies in Kenya and Tanzania in 1998. These fears escalated after the September 2001 terrorist attacks on New York and Washington, DC. In October 2001, the UN included Itihaad on a list of organizations associated with al-Qaeda, and in December the United States placed al-Itihaad on the 2001 USA Patriot Act’s “Terrorist Exclusion List.” Businesses with purported ties to al-Itihaad were also targeted. Among these was Somalia’s largest employer, al-Barakat, a money transfer company with telecommunica-tions, internet, and other holdings that had assumed significant banking functions after the collapse of the country’s banking system in the early 1990s. Al-Barakat had operations in forty countries, transferred some
$140 million annually, and served as a lifeline for many Somalis, who depended on remittances from family members abroad to sustain them.
In November 2001, the George W. Bush administration, claiming that al-Barakat served as a conduit for funds to al-Qaeda, closed its offices, froze its US assets, and pressured the UN Security Council to impose sanctions.14 These actions effectively terminated al-Barakat’s operations, jeopardizing the well-being of Somali citizens and generating increased animosity toward the United States.15 Washington also sought common cause with Ethiopia, Somalia’s regional rival, which for centuries had been dominated by Christian elites. In 2006, the US government referred to Ethiopia as “the linchpin to stability in the Horn of Africa and the Global War on Terrorism.”16
Instability in Somalia also worried other external powers. The UN, the AU, the EU, the Arab League, and IGAD intensified their diplomatic
involvement. In 2004, they helped broker an agreement to establish a central government in Somalia—the fourteenth attempt since Siad Barre was ousted in 1991. The resulting Transitional Federal Government was backed by these external entities, and by the United States and Ethio-pia. However, the TFG had very little support inside Somalia. The nego-tiations had been deeply influenced by SRRC warlords who aspired to establish a clan-based federal system that would consolidate their own power. Although presented as a government of national unity, the TFG was dominated by the Mijerteen clan/Darod clan family of its presi-dent, SRRC warlord Abdullahi Yusuf Ahmed. It marginalized many of the Hawiye clans that had long controlled Mogadishu, and it purged the parliament of opposition members. Unable to enter Mogadishu’s hos-tile environs, the TFG established its capital in Baidoa, 150 miles away, where it was protected by Ethiopian troops. It controlled little territory outside that city. Rife with nepotism and cronyism, the TFG was incom-petent and corrupt. The salaries of senior army, police, and intelligence officers, as well as government ministers and parliamentarians, were paid by foreign donors, and government officials were not accountable to the Somali people. President Yusuf, the SRRC men he appointed to top positions, and his prime minister, Ali Mohamed Ghedi, were all closely linked to Ethiopia. As a result, many Somalis considered the TFG to be an Ethiopian puppet regime.
Supported by the United States, President Yusuf opposed all forms of political Islam and resisted the inclusion of Islamists in his govern-ment. As a result, the powerful Islamic courts and their proponents re-fused to support the TFG. President Yusuf’s reliance on Ethiopian troops and his anti-Islamist actions helped rally support for the Islamic Courts Union (ICU), which had formed in 2000 to consolidate the power of the Islamic courts and improve their effectiveness. Courts affiliated with al-Itihaad promoted a strict, Salafist interpretation of Islamic law, while others interpreted the law according to the more tolerant Sufi traditions that most Somalis embraced.17
Disregarding popular support for the ICU, external powers were de-termined to undermine it. In early 2006, the CIA encouraged a group of clan militia leaders, businessmen, and warlords—including four TFG cabi-net ministers—to join forces against the growing Islamist movement. The result was the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT). Violating the 1992 UN arms embargo, the CIA provided the
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ARPCT with weapons and financed its militias. In return, the alliance became an accessory to the US war on terror—capturing and render-ing to the United States suspected al-Qaeda operatives, specifically those believed to be involved in the 1998 US Embassy bombings in Kenya and Tanzania and the 2002 attacks on an Israeli-owned hotel and airliner in Kenya. Fighting between the ARPCT and the ICU broke out in February 2006. In May, warlord attacks on ICU militias in Mogadishu instigated some of the worst street fighting in the capital since Siad Barre’s govern-ment fell apart in 1991. The TFG appealed for foreign military assistance and the United States, Ethiopia, Italy, and Yemen complied, again violat-ing the UN arms embargo. Eritrea, in turn, provided weapons to the ICU militias to counter the influence of Ethiopia, its regional nemesis. In early June, ICU militias seized control of Mogadishu and ousted the warlords who had controlled the capital for fifteen years.
By July 2006, ICU militias had gained ascendancy over most of southern and central Somalia, including the key ports and airfields. In Mogadishu, the courts began to rebuild basic government services, es-tablishing committees on sanitation, reconstruction, education, and justice. They cracked down on criminals, armed youth, and warlord Photo 4.3. Ethiopian troops participate in AMISOM patrol in Baidoa, Somalia, March 27, 2014. Photo by Abdi Dagane/AU UN IST.
militias, bringing a semblance of security to the capital city. Mogadishu’s port and international airport, which had been closed for more than a decade, reopened. The ICU garnered immense popular support, even from secular Somalis who welcomed the implementation of Islamic law as way to stem crime and violence. François Lonseny Fall, at that time the UN special representative to Somalia, acknowledged that the ICU had “achieved great things in Mogadishu,” while other human rights groups claimed that with Islam as a unifying factor, the ICU had been more successful than any previous government in uniting and disarm-ing Somali clans.18
The ICU victory was precisely the opposite of what the CIA had hoped for when it backed the warlord alliance. In fact, foreign meddling had triggered a backlash that strengthened radical factions. In June 2006, Sheikh Hassan Dahir Aweys, a Salafi and former al-Itihaad leader, was appointed chair of the ICU consultative council, challenging the leader-ship of the executive council chair, Sheikh Sharif Sheikh Ahmed, a mod-erate Sufi cleric. A Somali national army colonel under Siad Barre and onetime member of Aidid’s militia, Aweys had joined the al-Itihaad mili-tia in the early 1990s and helped establish Islamic courts in Mogadishu at the end of that decade. Although Aweys hoped to implement Islamic law throughout Somalia, some analysts considered him to be a mitigating in-fluence vis-à-vis extremists in al-Shabaab, the ICU’s youth militia, which aspired to establish an Islamic state beyond Somalia’s borders.
External support for the warlords and the TFG strengthened the po-sition of radicals in the ICU. In early July 2006, Osama bin Laden called on Muslims worldwide to wage jihad in Somalia and warned that Mus-lim fighters would challenge all foreign troops, including UN and AU peacekeepers, if they intervened to support the TFG. Three weeks later, when ICU forces threatened the transitional government’s headquar-ters in Baidoa, hundreds of Ethiopian soldiers, supported by tanks and helicopters, arrived to protect the government’s position. In the weeks that followed, some 5,000 Ethiopian troops invaded Somalia, while more amassed on the border. ICU hardliners began to mobilize for confron-tation with Ethiopia, appealing both to Somali irredentist claims and to religious sentiment against the predominantly Christian regime that sus-tained the warlords and propped up the TFG.
Although most Somalis did not support the jihadist agenda of the hardliners, and few wanted another war with Ethiopia—which still
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claimed one of the largest, most sophisticated armies in sub-Saharan Africa—the presence of Ethiopian troops in Baidoa and persistent Ethiopian incursions across Somalia’s borders rallied the population be-hind the radicals. Moderates in the ICU, who previously had discussed elections and power sharing, also began talking war. Departing from his earlier position, Sheikh Hassan Dahir Aweys urged Somalis to prepare for jihad against Ethiopia. In late July and early August 2006, some forty senior government officials, including a number of cabinet ministers, abandoned the TFG. Some defected to the ICU, taking their own militias with them.
The fallout from foreign intervention rapidly transformed the So-mali conflict into a regional conflagration. In October, the UN reported that ten nations were supplying arms to various Somali factions in vio-lation of the UN embargo. Djibouti, Egypt, Eritrea, Iran, Libya, Saudi Arabia, and Syria were supporting the ICU, while Ethiopia, Uganda, and Yemen were furnishing weapons to the TFG. In November, as ICU mi-litias routed TFG forces in the north, President Yusuf appealed for fur-ther external assistance. The United States responded, pushing through a UN Security Council resolution on December 6, 2006, that described the Somali situation as “a threat to international peace and security in the region” and authorized the AU and IGAD to establish a military force to protect the TFG and to train its security forces.19 The resolution also created a loophole in the UN arms embargo that allowed the African peacekeeping forces—and implicitly, Ethiopian soldiers protecting the TFG—to be supplied with weapons, while continuing to deny arms to the ICU.
On December 14, US Assistant Secretary of State for African Affairs Jendayi Frazer referred to ICU leaders as “extremists to the core” who were “controlled by al-Qaeda.”20 Ethiopia took this high-level US con-demnation as a green light for a full-scale invasion. Six days later, as ICU militias attempted to capture Baidoa, Ethiopian warplanes buttressed by thousands of Ethiopian and TFG soldiers struck back, decimating the poorly armed ICU militias. On December 24, 2006, after months of military buildup, some 8,000 Ethiopian troops, supported by tanks and attack helicopters, advanced on Mogadishu, bombing Somalia’s two main airports along the way. The UN Security Council was silent. Its failure to condemn the Ethiopian invasion confirmed Somali views that the international body was not a neutral broker of peace, but a partisan
force that had sanctioned foreign intervention to bolster a client regime that had virtually no internal support.
While the UN tacitly condoned the Ethiopian offensive, the United States actively supported it. The State Department referred to the inva-sion as a legitimate response to aggresinva-sion by Somali Muslim extremists.
Convinced that the al-Qaeda militants who had planned the 1998 and 2002 attacks in Kenya and Tanzania were hiding in southern Somalia under ICU protection, US intelligence officials were determined to root them out. The Combined Joint Task Force–Horn of Africa (CJTF-HOA), a Djibouti-based counterterrorism entity comprising nearly 2,000 US military and civilian personnel, provided satellite photos and other in-telligence to the Ethiopian army to help it locate ICU fighters. Planes piloted by US Special Operations Forces took off from bases in Djibouti, Ethiopia, and Kenya and joined Ethiopian aircraft in bombing ICU strongholds. As the invasion progressed, US Special Operations Forces, functioning from a secret airfield in Ethiopia, entered Somalia alongside the Ethiopian army, purportedly to track down the al-Qaeda suspects.21 US ground troops helped Ethiopian soldiers gather evidence, while the US Navy patrolled the Somali coast and intercepted ships to search for al-Qaeda operatives. Fearing massive bloodshed and the destruction of Mogadishu, business and clan leaders urged the ICU to disband and to abandon the capital without resistance. The ICU militias complied and retreated toward the Kenyan border, pursued by intelligence and security forces from Ethiopia, Kenya, Somalia, and the United States. In a rendi-tion program run by Ethiopia, the United States, and the TFG, militants were rounded up and deported to secret detention facilities in Ethiopia.
On January 8, 2007, TFG President Yusuf entered the capital for the first time since taking office in 2004.
The joint Ethiopian-US operation resulted in an increase, rather than a decrease, in chaos and violence. Within weeks of the foreign inva-sion, a homegrown insurgency had begun, rallying al-Shabaab and other ICU militias, clans that had been marginalized by the TFG, and a wide range of groups that benefited from anarchy, including warlord militias, hired gunmen, arms and drug traffickers, smugglers, and profiteers. The Somali insurgents were joined by fighters from Afghanistan, Pakistan, and the Arabian Peninsula who responded to the call to wage jihad against Ethiopia. Warlord and clan militias set up roadblocks and shook down residents. Banditry and extortion, which had been suppressed by
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the ICU, returned with a vengeance. Using weapons left over from the Cold War, including AK-47 assault rifles, mortars, and rocket-propelled grenades, insurgents attacked TFG and Ethiopian troops, government buildings, and infrastructure. Employing techniques developed by Iraqi resisters after the 2003 US invasion, they discharged landmines, suicide bombs, and improvised explosive devices, and they targeted TFG offi-cials for assassination. In mid-January 2007, the TFG parliament de-clared a state of emergency and granted the president broad powers to enforce security.
Foreign involvement assumed a new dimension in February, when the UN Security Council authorized the establishment of the African Union Mission in Somalia (AMISOM), which was slated to deploy 8,000 African peacekeepers of diverse nationalities to replace the Ethiopian soldiers shoring up the TFG. Funded by the UN and the EU, the AU force appeared to many Somalis as yet another case of unwanted foreign in-trusion. The fact that most of the troops came from the predominantly Christian countries of Uganda and Burundi augmented public hostility.
Moreover, the AU force was slow to arrive—only 2,600 soldiers were in place by August 2008. As a result, Ethiopian soldiers would remain on Somali soil until early 2009.
In March 2007, the Ethiopian military launched an offensive on Mogadishu to capture key locations from insurgents who had held parts of the capital since the ICU’s departure in January. Assisted by TFG police, Ethiopian soldiers cracked down on Hawiye neighborhoods and closed ports and airfields belonging to Hawiye businessmen, charging that the clan was supporting the insurgency. Widespread ar-rests, assaults, looting, and rape—perpetrated both by Ethiopian soldiers and by TFG police who were trained and paid by the UN Development Programme—intensified popular support for the insurgency.
The ensuing two-month-long battle for Mogadishu precipitated the most destructive fighting in a decade and a half. By the end of April, some 1,300 Mogadishu residents had been killed, and more than 400,000 had fled their homes. Human rights organizations accused participants on all sides of war crimes. They charged that Ethiopian forces had engaged in widespread and indiscriminate bombing of densely populated areas as well as the collective punishment of civilians, including mass arrests and summary executions. They also claimed that the Ethiopian military had intentionally shelled hospitals, pillaged medical equipment, and blocked
the flow of humanitarian assistance, and that Ethiopian and TFG sol-diers had raped, plundered, and killed with impunity. Human rights groups asserted that insurgents had also engaged in assassinations and summary executions and that they had demonstrated disregard for ci-vilian lives by mounting attacks from densely populated neighborhoods, which then bore the brunt of Ethiopian and TFG retaliation.
Violence continued to escalate throughout 2007. Badly weakened by infighting and defections, the TFG was on the verge of collapse. By Janu-ary 2008, al-Shabaab, other ICU militias, and their allies had recovered much of the territory they had lost a year earlier. Al-Shabaab garnered some civilian support, especially in southern Somalia, where it estab-lished a semblance of law and order and a justice system that followed years of abuse by warlord militias and government police. In March 2008, the US State Department designated al-Shabaab a “foreign terrorist organization.”22 Critics warned that the label could enhance al-Shabaab’s popularity and at the same time render negotiations with the organiza-tion nearly impossible. Matters were further complicated in May, when a
Violence continued to escalate throughout 2007. Badly weakened by infighting and defections, the TFG was on the verge of collapse. By Janu-ary 2008, al-Shabaab, other ICU militias, and their allies had recovered much of the territory they had lost a year earlier. Al-Shabaab garnered some civilian support, especially in southern Somalia, where it estab-lished a semblance of law and order and a justice system that followed years of abuse by warlord militias and government police. In March 2008, the US State Department designated al-Shabaab a “foreign terrorist organization.”22 Critics warned that the label could enhance al-Shabaab’s popularity and at the same time render negotiations with the organiza-tion nearly impossible. Matters were further complicated in May, when a