Islamic Courts Union

The Islamic Courts Union (Midowga Maxkamadaha Islaamiga) was a legal and political organization founded by Mogadishu-based Sharia courts during the early 2000s to combat the lawlessness stemming from the Somali Civil War. By mid-to-late 2006, the Islamic Courts had expanded their influence to become the de facto government in most of southern and central Somalia, succeeding in creating the first semblance of a state since 1991.

Following the collapse of the Somali Democratic Republic in early 1991, a new phenomenon emerged – the establishment of Sharia courts to impose law and order on the volatile neighborhoods of Mogadishu. These independent courts found their existence threatened by warlords, necessitating cooperation which resulted in their unification by 2000. The Islamic Courts Union (ICU) was a broad-based organization comprising various courts with diverse goals, from national political ambitions to local dispute resolution and promoting Islam. Because of Somalia's deep attachment to Islam, the initiative widely gained popularity and acceptance, along with significant financial backing from the Somali business community. By originating from the grassroots level, reconstituting the Somali state, asserting their governance under the mantle of religious impartiality and eliminating the widely despised warlords controlling much of the city - the ICU gained the confidence of a populace exhausted by warfare.

During the summer of 2006, the ICU decisively defeated a warlord alliance funded by the CIA and became the first entity to consolidate control over all of Mogadishu since the collapse of the state. The period that followed is widely heralded as the most stable and productive period Somalia had seen up to that point since the outbreak of the civil war. Residents of Mogadishu were finally able to move around the city without fear of attack, the international airport and seaport were opened for the first time in over a decade, a massive debris clean up campaign was started and there was a significant reduction of arms on the streets.

Six months into their reign, the Islamic Courts Union was toppled during the final days of 2006 by a full scale Ethiopian invasion of Somalia, supported by the United States. Much of the organizational structure of the ICU disintegrated early on in 2007 due to the invasion as the ENDF/US forces brought the Transitional Federal Government (TFG) to power. Following the collapse of courts rule, much of the high ranking leadership sought refuge in Eritrea. In the insurgency that followed, a youth militia within the military wing of the Islamic Courts, Al-Shabaab, stayed behind and broke away, initially greatly empowering themselves as a popular resistance movement against the occupation. During 2007 and 2008, ICU forces participated in the insurgency against Ethiopian troops occupying Somalia. High-ranking members of the Islamic Courts later founded the Alliance for the Re-liberation of Somalia (ARS) in late 2007, which would merge with the TFG in late 2008. Former chairman of the Islamic Courts Union, Sharif Sheikh Ahmed, became president of Somalia in 2009, replacing successfully the Transitional Government with the Federal Government of Somalia. In 2012, the country adopted a new constitution that declared Somalia an Islamic state with Sharia as its primary source of law.

Historical background
Islamic law (Sharia) was used during the reign of the Somali Ajuran Sultantate. After existing for about 300 years, it declined during the 17th century after abandoning Sharia and becoming oppressive. During the 19th century, before the Scramble for Africa had arrived to Somali territories, Sharia courts headed by qadis (Islamic judges) operated all along the coast.

During 1990, just before the full outbreak of the Somali Civil War, a group of sixty highly prominent members of Somali society under the banner of "Islamic Call" published a public manifesto addressed to President Mohammed Siad Barre. The manifesto warned that he had committed serious transgressions against the laws of Islam and called for him to peacefully step down and transition power, but their attempts were unsuccessful.

First Sharia Courts
The first appearance of Sharia courts to build local stability began immediately after the state completely collapsed in January 1991. In the weeks following the total collapse, militias that had toppled the government began hunting down civilians based off their clan identity. Around this time, several well-known Somali scholars such as Sheikh Sharif Sharafow, Sheikh Ibrahim Suley and Sheikh Mohamed Moallin Hassan established Sharia courts in order to rescue these civilians from attack and to address the rising lawlessness. The first Shari'a courts were started on a very small local neighborhood level by Somali religious leaders as a way to address issues in their communities. Most problems they dealt with were related to petty crimes and family disputes. In the chaotic political context of war torn Mogadishu the religious leaders were considered by most Somalis as some of the only people who could be trusted to impartially resolve disputes. Importantly, the courts also did not take positions on national-political or clan affairs, lending significant credence to their purported impartiality.

Around the same time as the creation of the Mogadishu courts, Sheikh Mohamed Haji Yusuf and Sheikh Mohamud A. Nur established a new Islamic court in the Luuq district of Gedo region during 1992. The court had more success than its counterparts in Mogadishu, and consequently Luuq district was the safest area in Somalia during much of the 1990s. The court was later dissolved in 1997 when the Somali National Front and Ethiopian military collaborated to topple it.

The Sheikh Ali–Dhere court
In 1994, the opening of a court in Mogadishu run by a Sheikh named Ali Dheere had a significant impact on the expansion of the Sharia courts system in the city. Dheere, who lived in one of the most dangerous regions of war-torn Mogadishu, became exhausted with the growing anarchy. He decided to put his religious training to use by setting up the first major Sharia court in Somalia. The infamous "Siisii Street" ran through his community and became notorious for its dangerous reputation.

"Siraadka Qiyaama iyo Siisii Allow na mooti (Translation: 'Oh god save me from the troubles that are associated with the day of judgement and those of Siisii Street')"

Primarily his court focused on aiding merchants and store owners resolve their disputes, helping people arrange legal agreements for large purchases like homes, and trying people for crimes. Local scholars, elders, businessmen and political leaders cooperated with Dheere in a bid to end the spiraling chaos in their community. Soon Ali Dheere had a staff that apprehended bandits and thieves in the area to bring them to be put on trial. His success in bringing order to his neighborhood in Mogadishu became well known throughout the city and led to the establishment of other copycat Sharia courts. The court did not shy away from strict punishments and even carried out executions. Soon word began rapidly spreading that law and order was being established in Dheeres sector of the city and the crime rate in the area subsequently dropped dramatically.

Rise of the Mogadishu Islamic Courts
In 1994 and 1995 other Sharia courthouses began opening up in northern Mogadishu, operating independently in their own self contained jurisdictions in the city. During these early years the courts began gaining considerable support for deploying security forces to protect schools and hospitals from warlord incursions and predatory bandits. Before the establishment of these courts, acts of rape had become commonplace in north Mogadishu since 1991. The establishment of the judiciary made a considerable impact on the security situation as the courts made a point of handing out the capital punishment of stoning to rapists. By 1997 there had been seven cases of execution by stoning in Somalia. It has been noted that suppression of war time sexual violence was a major underlying factor in Somali women's support for the Islamic Courts.

The first court did not start in southern Mogadishu until 1998, as the de facto ruler of the territory, General Mohammed Farah Aidid and his faction the Somali National Alliance opposed the Islamic courts, and no progress occurred until after Aidids death. Ali Mahdi, Aidids prime rival controlling the northern part of the city, issued a decree to dismantle Ali Dheere's Court after perceiving the Sheikhs rising popularity as a threat to his own authority. As the years passed, with nothing but warlords offering to replace its authority, the rule of the sharia courts began to cement.

By 1999 the multiple Islamic courts had jurisdiction over much of the south of the city as well and five active Sharia courts were operating in the region. The courts were not an organized movement or a government, but represented the closest thing Somalia had to either. Their influence was enhanced by financial donors abroad who sought to bring any semblance of stability to the country. While many Somalis voiced disapproval of the more fundamentalist ways of the original Sharia courts, it was noted that most felt that they were well organized and effective civil administrators.

Consolidation of Islamic Courts
In April 1999, several Sharia courts united for the first time, taking control of Mogadishu's Bakaara Market from the local warlords. By the end of the year, their joint efforts had successfully cornered numerous warlords to the outskirts of Mogadishu, although they lacked the resources to completely dominate the city.

By 2000, having liberated a significant portion of the city from warlord control, eleven of these individual Sharia courts amalgamated to establish the Islamic Courts Council. This consolidation led to the unification of their militias into a single combat force. This development marked a pivotal moment in the civil war, as it signified the emergence of the first major non-warlord affiliated Somali force in the city. A 'Shari’ah Implementation Council' was created that same year, which began to consolidate resources and power on the basis of Islamic doctrine instead of clannism. Professor Mark Fathi Massoud draws a comparison between the Somalis' late 1990s and early 2000s turn towards local religious courts for self-governance and the historical patterns observed in early democratic Western Europe and colonial North America. In both cases, the establishment of courts and the invocation of the divine played crucial roles in state-building. Massoud highlights that the Sharia courts' use of religion to foster stability has parallels with those courts that significantly influenced the nascent phases of democratic states.

When the Transitional National Government of Somalia was established in Djibouti during the spring of 2000 the momentum of the ICU was slowed. It would not return until it was revived in 2004 by Sheikh Sharif Sheikh Ahmed who was subsequently elected as chairman of the ICU. The year before in 2003, Sheikh Sharif Ahmed had been a school teacher that had become frustrated with the return of insecurity in north Mogadishu and successfully pushed to rejuvenate the Islamic Courts system in the region. Following the failure of the Transitional National Government of Somalia established in 2000, the Transitional Federal Government (TFG) led by Abdullahi Yusuf was formed in 2004. Previously aligned closely with Ethiopia, Yusuf's leadership received significant support from the Ethiopian government. This support was believed to be pivotal in his electoral victory for the TFG leadership in an election held in Kenya. Before becoming president of the TFG during 2004, Abdullahi Yusuf was a member of an Ethiopian-backed coalition of warlords that had undermined a previous attempt at restoring a government in Somalia when the Transitional National Government (TNG) formed in 2000. Professor Jude Cocodia, a political science scholar from Niger Delta University, notes that Ethiopia's deep involvement in the formation of the TFG led many Somalis to view the government as inauthentic and essentially a puppet regime under Ethiopian influence. This sentiment was further amplified by historical events, such as the 1982 Border War, during which Yusuf led the Somali Salvation Democratic Front (SSDF) and collaborated with invading Ethiopian forces.

The TFG operated entirely outside of Somalia due to instability in Mogadishu and consequently was criticized by Somali citizens and international community. At the time the TFG was only recognized by Kenya and Ethiopia, as the European Union, the United States and other members of the international community refused to fully recognize the TFG's legitimacy until it operated from Mogadishu. To counter this, the TFG moved into Somalia for the first time in 2005, eventually setting up its headquarters south west of Mogadishu in Baidoa.

Islamic Courts Union – Warlord alliance conflict
As the courts started to unify in the early 2000s, tensions escalated with the warlords. Within the framework of the War On Terror, the U.S. government perceived the rise of an Islamic movement in Somalia as a potential terror risk. From 2003 onwards, the Central Intelligence Agency (CIA) initiated covert operations against the Islamic Courts Union, aiming to depose them from power. The union consisted of about eleven courts in this period. The Economist described the ICU as more tolerant than the Taliban and noted that the majority of the Islamic Courts operated on a 'traditionally tolerant Sufi-infused brand of Islam'. According to a report by Ted Dagne, an Africa Research Specialist for the Congressional Research Service,"'...the leadership [of the ICU] was often referred to as jihadist, extremist, and at times terrorist by some observers without much evidence to support the allegations. For example, the assessment of the Islamic Courts by U.S. officials was that less than 5% of the Islamic Courts leadership can be considered extremist, according to a senior State Department official.'"

CIA intervention
During 2003, the American Central Intelligence Agency began covert operations targeting the Courts. The Bush administration had become increasingly concerned with the growing power of the Islamic Courts Union, and feared that they would make Somalia a haven for Al-Qaeda to plan attacks from, like in Afghanistan. American support for the warlords extended to the point where, on numerous occasions, Nairobi-based CIA officers landed on warlord-controlled airstrips in Mogadishu with large amounts of money for distribution to Somali militias. According to John Prendergast, CIA-operated flights into Somalia had been bringing in $100,000 to US$150,000 per month for the warlords and he further claimed that the flights remained in Somalia for the day so that CIA agents can confer with them. The CIA also gave its newfound allies surveillance equipment for "tracking al Qaeda suspects". According to multiple U.S. officials, the decision to use of the warlords as proxies was born from fears of once again committing large numbers of American soldiers to Somalia following the disastrous 1993 Battle of Mogadishu. Many of the warlords the Americans funded to fight the Islamic Courts Union were many of the same ones that had fought directly against the Americans in Mogadishu during UNOSOM II in 1993.

Military capacity
The ICU did not maintain a significant fighting force as the organization was overwhelmingly focused on providing legal and social services. The deficiency in firepower was especially pronounced in heavy weaponry. According to senior Islamic court officials the union only possessed a total of four technical improvised fighting vehicles when the 2006 Battle of Mogadishu against the Somali warlord alliance broke out.

Warlord conflict and CIA escalation
Beginning in 2005 Mogadishu was hit by a significant wave of unexplained assassinations and disappearances. The Islamic Courts claimed that covert US government operations and warlords were targeting high ranking ICU officials. According to C. Barnes & H. Hassan, "It was in this context that a military force known as Al-Shabaab (‘the Youth’) emerged, related to but seemingly autonomous of the broad based Courts movement." At the time it was widely believed in Mogadishu that Somali warlords were cooperating with U.S. intelligence agents to kidnap alleged terror suspects, particularly prominent religious leaders. This atmosphere forced the ICU to take a more confrontational stance against the warlords. The CIA backed warlords had a notorious pattern of seizing innocent clerics with little or no intelligence value, which greatly fed into the already existing perception among Somalis that the Americans and the warlords were waging a war against Islam under the guise of the War on Terrorism. During 2006, at the suggestion of the Central Intelligence Agency (CIA), anti-ICU warlords united under the banner of the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT). The decision to support these warlords generated dissent within the CIA, the US State Department, and European states. Many officials expressed apprehensions that this backing could lead to a major anti-American backlash in Somalia and greatly empower Islamist factions. As fighting for the city was ongoing in March 2006, the courts succeeded in seizing critical roads and infrastructure from the ARPCT. Prominent locals had urged the ICU and the warlord alliance to agree to a ceasefire to prevent bloodshed in Mogadishu. The ICU pledged to abide by a ceasefire, but mediators between the two organizations reported that the warlord alliance had delayed and refused to commit themselves. The Americans approved greater funding for the Somali warlords and further encourage them to counter the ICU, a decision made by top officials in Washington which was later reaffirmed by the U.S. National Security Council during meeting about Somalia in March 2006. At the time of the meeting there was fierce fighting in between the warlords and the Islamic Courts around Mogadishu, and the decision was taken to make counter-terrorism the top policy priority for Somalia.

A public uprising occurred in support of the Courts against the warlord alliance. The ICU enjoyed widespread support from Mogadishu citizens and business community against the warlords, greatly aiding its ability to seize and control large swathes of the city. The broad support of Somali women for the union played a significant role in the organizations ability to maintain combat operations against the warlords. In the view of Mary Harper, a journalist with BBC Africa, the Islamic Courts Union was in reality more of a loose federation and only began to unite into a homogeneous body with a clear authority when its existence was threatened by the ARPCT. The Transitional Federal Government of Somalia, being both in contention with the ICU and backed by the United States, openly opposed the Americans operation to fund the warlords. Despite significant opposition in the government, several members of the CIA backed warlord alliance were holding senior posts within the TFG while fighting against the ICU was ongoing.

By April 2006 much of Mogadishu had fallen under the control of the ICU after clashes with the warlord alliance. The cities air and seaports came under the organizations direct control for the first time. In May they seized the very building where the warlord alliance had been founded and established an Islamic Court in its place. Two of the defeated warlords allegedly fled to an American naval vessel off the Somali coast according to witnesses in Mogadishu.

Defeat of the warlord alliance and seizure of Mogadishu
On 5 June 2006, the Islamic Courts Union decisively defeated the warlord alliance in the Second Battle of Mogadishu, gained total authority over the capital and proceeded to establish a 65-mile radius of control around the city. This was a seminal moment in modern Somali history, as the ICU was now the first group to have consolidated control over all of Mogadishu since the collapse of the Somali state. According to Chatham House, "The Courts achieved the unthinkable, uniting Mogadishu for the first time in 16 years, and re-establishing peace and security". The Alliance for the Restoration of Peace and Counter-Terrorism soon collapsed, with the majority of its commanders publicly resigning or expressing support for the ICU. BBC News reported that the ICU had emerged as Somalia's strongest and most popular faction.

"The Union of Islamic Courts was established to ensure that Somali people suffering for 15 years would gain peace and full justice and freedom from the anarchic rule of warlords who refuted their people to no direction."

The leaders of the ICU repeatedly professed that they intended to negotiate with the Transitional Federal Government In Baidoa so that it could move into Mogadishu and reunite Somalia. Several days after the city came under ICU control, US State Department spokesman Sean McCormack noted that goal of the union was to "...lay the foundations for some institutions in Somalia that might form the basis for a better and more peaceful, secure Somalia where the rule of law is important." In mid June, ICU leaders sent a cable to Washington stating that the courts had no interest in being enemies with the United States.

Governance
Over the ensuing months, the eleven amalgamated Islamic Courts initiated a drive to establish stability in Mogadishu and the territories under its control. This period of the Somali Civil War, referred to as a 'Golden era' of Somali politics by top UN officials, saw the ICU undertake significant reformative and security measures.

Security and law
After coming in control of the entirety of Mogadishu, the ICU revived sixteen previously defunct police stations in the city, deploying nearly 600 personnel and dozens of vehicles to fortify the nascent law enforcement framework. This resulted in a steep drop in banditry within days, as thieves avoided areas within reach of the court forces. Community reintegration programs were offered to former militiamen, and in an effort to restructure the security wing, formalized military and police training was introduced to the different court forces. Additionally, the city witnessed a ban on the open possession of firearms unless registered with a court, and foreign visitors were publicly advised to provide two weeks' prior notice of their arrival for their security.

The ICU created a coast guard and pirate activity completely ceased due to aggressive anti-piracy operations. According to courts officials, the organization was sending large contingents of troops into the central Somali regions to crack down on pirate operations based there. In one notable incident, ICU forces stormed a hijacked United Arab Emirates registered ship, and recaptured it after a battle with the pirates aboard the vessel.

The courts also began issuing travel visas, resulting in significant influx of investors and former refugees. Another action that significantly increased the ICU's popularity was the restoration of proper ownership regarding land and homes that had been lost or stolen during the civil war. It was noted that as the courts were taking over the city many people simply left the homes they occupied before the rightful owners had even taken their cases to the specialized Sharia courts that were setup for property disputes. During this period the ICU also began to expand its authority by validating major transactions such as the purchase of vehicles or homes and overseeing marriages and divorces.

Social and economic
Commenting on the state of education in the wake of the takeover, The Economist observed that, "...school attendance is rising, particularly among girls." During the ICU's brief control of southern Somalia, the organization made numerous declarations condemning discrimination against what the courts considered to be "oppressed clans" (e.g., Yibir, Madhibaan and Jareer) as un-Islamic and haram. The courts deliberately orchestrated marriages between women from discriminated groups to men from larger Somali clans in order to challenge popular perceptions. While many of the initial Mogadishu courts were linked to the Hawiye clan, the ICU took deliberate measures to ensure clan bias did not influence legal proceedings. This approach ultimately earned them a reputation for impartiality. The Courts made efforts towards patching together neighborhoods that had been divided by the civil war.

Mogadishu International Airport, closed since the withdrawal of UNOSOM II forces in 1995, was reopened by the courts on July 15, 2006. On August 25, the historic seaport, once one of the busiest in East Africa, was also reopened by the courts, marking a crucial step in revitalizing the region's economic infrastructure. By 19 June 2006, the ICU founded several clinics and schools in the city. The formation of a sanitation committee and the organization of a substantial clean-up campaign on 20 July 2006 resulted in the first clearing of war debris and rubbish from Mogadishu's streets in over a decade. This successful initiative was further expanded to regions surrounding the capital. In August 2006, the courts issued a directive imposing a ban on the export of rare birds and wildlife from Somalia. Simultaneously, a prohibition on charcoal exports was enacted, driven by the alarming rate of deforestation occurring across the country due to the practice.

The courts secured broad support from the Mogadishu business community by addressing issues such as theft and extortion, creating a more favourable environment for trade. As they advanced through southern Somalia, the ICU eliminated all militia checkpoints on the 'Baidoa Corridor,' a vital transport and trade route to Kenya. Under the courts' administration, transportation costs on the corridor plummeted by 50%. Traders involved in studies on the route hailed the period under ICU control as a 'golden era of overall land trade.' Additionally, the courts focused on enhancing traffic flow in Mogadishu, deploying personnel to regulate traffic and dismantle roadblocks at major roads and junctions. Consequently, the following weeks witnessed a noteworthy decline in the prices of goods. Researchers conducting fieldwork in Somalia during May 2023 observed that some of the only banknotes still circulating in the country were ones issued by the ICU government over a decade and half earlier.

Islamic Courts expansion and Ethiopian invasion (June–September 2006)
British television station Channel 4 acquired a leaked document detailing a confidential meeting between senior American and Ethiopian officials in Addis Ababa six months prior to the full scale December 2006 invasion. Participants deliberated on various scenarios, with the 'worst-case scenario' being the potential takeover of Somalia by the Islamic Courts Union. The documents revealed that the US found the prospect unacceptable and would back Ethiopia in the event of an ICU takeover. Journalist Jon Snow reported that during the meeting ‘the blueprint for a very American supported Ethiopian invasion of Somalia was hatched’. No Somali officials were involved in the discussions. Pentagon officials and intelligence analysts reported that the invasion had been planned during the summer of 2006 and that US special forces were on the ground before the Ethiopians had intervened.

With its newfound position of authority, the ICU seized on its popularity and began pushing deep into the regions surrounding the city for the first time. Their offensive capability was greatly aided by new weaponry it had captured from the CIA backed warlord alliance. The Islamic Courts movement found significant support across Somalia. According to Prof. Abdi Ismail Samatar, "...the enthusiasm of the population for change, was such that far off regions in the country, like Somaliland and Puntland, felt pressure and pronounced that they would use Sharia as a basis for governing their regions." Many Somalis across the nation held fundraising drives at mosques for the Islamic Courts. Several hundred men from Somaliland joined the Courts militia, while the contribution from ICU supporters in Puntland was primarily financial and logistical. During the summer of 2006, the ICU was allegedly being given support by Eritrea, Djibouti, Iran, Libya, Egypt, Saudi Arabia and Syria.

First Ethiopian incursions
The Ethiopian invasion began with the dispatch of several thousands troops around Baidoa city located in Bay region, far inside Somalia, in order to build a bridgehead for a future large scale military operation. On 16 June 2006, Shabeelle Media Network reported that sources in Ethiopia's Somali Region had witnessed a massing of ENDF 'heavy armoured vehicles' along all the border towns on the Ethiopian–Somali border. The following day on 17 June, local Somali officials and residents in Gedo region reported about 50 Ethiopian armored vehicles had passed through the border town of Dolow and pushed 50 km inland near the town of Luuq. Although the Ethiopian government denied claims of ENDF forces crossing the border, residents in towns within Somalia reported encounters with Ethiopian troops inquiring whether the ICU had reached the area.

ICU head Sheik Sharif Sheik Ahmed claimed that 300 Ethiopian troops had entered the country through the border town of Dolow in Gedo region that morning in support of the TFG, and that Ethiopian forces had also been probing Somali border towns. He would go on to threaten to fight Ethiopian troops if they continued intervening and further stated, “We want the whole world to know what’s going on. The United States is encouraging Ethiopia to take over the area. Ethiopia has crossed our borders and are heading for us.”  Sharif stated that the courts had no intention of attacking Ethiopia, but claimed that Ethiopian forces had 'brought war' by beginning an incursion into Somalia. The Ethiopian government would deny the deployment of its forces in Somalia and countered that the ICU was marching towards its borders. The TFG denied accusations of an Ethiopian military deployment counter claiming that ICU was fabricating a pretext to assault its capital in Baidoa.

On June 24, Hassan Dahir Aweys was named head of the ICUs newly formed 88 member parliament, the Council of the Islamic Courts. Several days later Aweys stated in an interview with Agence France Presse, "We are ready for partnership with the Americans. We would like to work with them if they respect us and stop interfering with Somali internal affairs,"

Khartoum ICU/TFG talks
The TFG, overshadowed by the achievements of the ICU, was in dire need of the popularity and military capacity of the courts and the ICU in turn was in need of international recognition, along with the political and administrative skills required to run a government that the TFG possessed. The obvious deficiencies of both organizations led many to perceive a possible complimentary ICU/TFG amalgamation. Secretary-General of the United Nations, Koffi Annan, urged the ICU and TFG to unite and form a government in order to attain a lasting peace in Somalia. In late June, the UN formally created a contact group to directly communicate with the Islamic Courts. The Associated Press reported that the development reflected a growing realization within the UN that the ICU was the first serious governing body to appear since the collapse of the Somali state in 1991.

First Khartoum meeting (June 2006)
The Arab League arranged a conference between the ICU and TFG in June 2006 to discuss merger proposals in Khartoum, Sudan. The talk initially began positively but rapidly collapsed over the issue of Ethiopian forces deployed to Somalia at the request of the TFG. The ICU insisted that the presence of Ethiopian forces was the priority and should be dealt with first, while the TFG insisted that an agreement on a unified government had to be made before removing the Ethiopian presence. Neither side was willing to compromise on the issue of Ethiopian troops, leading to the collapse of the talks. On 22 June 2006 a communique was issued announcing that both parties recognized each other's legitimacy and that neither would engage in hostile propaganda against the other.

Both parties agreed to renew talks and meet again on 17 July 2006. During the talks another significant deployment of Ethiopian troops occurred on July 20, 2006, when they moved into Somalia. Local witnesses reported 20 to 25 armored vehicles crossing the border. The Ethiopian government once again denied the presence of any troops inside Somalia. Reuters estimated that roughly 5,000 ENDF troops had built up inside Somalia by this point. Two days later, another contingent of Ethiopian troops crossed into Somalia, leading to the collapse of the Khartoum peace talks between the ICU and TFG. Approximately 200 ENDF troops seized Wajid, taking control of the airport. Following the deployment at Wajid, the ICU walked out of talks with the TFG. Abdirahman Janaqow, the deputy leader of the ICU executive council, stated soon after that, "The Somali government has violated the accord and allowed Ethiopian troops to enter Somali soil." The TFG claimed that no Ethiopians were in Somalia and that only their troops were in Wajid. Soon after, residents reported two military helicopters landing at the town's airstrip. BBC News confirmed reports of Ethiopian troops in Wajid during interviews with local residents and aid workers. Following the towns seizure, the ICU pledged to wage a holy war to drive out ENDF forces in Somalia.

Second Khartoum meeting and collapse of talks
The TFG was alarmed by the rapid territorial expansion of the ICU and feared that it was attempting to encircle its capital in Baidoa. Neither party was willing to go to continue the Khartoum conference. The TFG insisted that the ICU withdraw to the territory it had occupied during the June conference, while the ICU demanded the withdrawal of Ethiopian military contingents in Somalia before discussions resumed. The two primary mediators, the Arab League and the Intergovernmental Authority on Development (IGAD) were both viewed as biased by the ICU and TFG. The ICU accused the IGAD of being partial to the TFG, while the TFG accused the Arab League of complicity with the ICU.

The ICU continued to gain territory around Baidoa and lacking any troops of its own the TFG requested foreign support. On 20 July 2006, Ethiopia deployed hundreds of troops to Baidoa. This prompted an immediate warning from Sheik Sharif Sheik Ahmed that the organization would invoke a jihad against Ethiopian forces if they did not withdraw. Numerous Somali witnesses and a BBC correspondent reported seeing Ethiopian Army trucks and hundreds of soldiers crossing the border and entering Baidoa. The TFG publicly denied the existence of Ethiopian forces in Baidoa and argued the claims were ICU propaganda. TFG minister of information Mohammed Abdi Hayir, claimed that sightings of Ethiopian forces in Somalia were a result of confused identity as Ethiopia had merely provided 4,000 uniforms to TFG forces.”  Eventually talks did resume, but in September instead of July 2006. Negotiations quickly broke down over the issues of Ethiopian forces and ICU expansion. According to former Somali diplomat and writer Ismail Ali Ismail, the failure of the second Khartoum talks stemmed from incompetent mediation, as he argues that the roadblock could have been resolved if the mediators had suggested and pushed for a simultaneous withdrawal of both ICU and Ethiopian forces under international supervision.

Escalation and full scale invasion (September–December 2006)
Before the full scale invasion began, more than 10,000 ENDF forces had been built up in and around Baidoa over the months since the first incursion in June 2006. By September, contingent of 7,000 Ethiopian troops had penetrated deep into Somalia. The Ethiopians had complete control over the TFG headquarters and had begun arming warlords defeated by the ICU.

On 18 September 2006, the first suicide bombing in Somali history occurred in the TFG capital of Baidoa, when a truck loaded with explosives attempted to assassinate President Abdullahi Yusuf. The ICU denied responsibility for the assassination attempt, instead pinning the blame on Ethiopian provocateurs. TFG Foreign Minister Ismail Hurre stated that whoever was responsible for the attack had wanted the ICU/TFG talks slated for 30 September 2006 to fail. Eventually the TFG, which had blamed previous attacks on warlords, for the first time accused radical elements within the ICU of the attack. 10 days before the assassination attempt had occurred, Baidoa warlord Mohamed Ibrahim Habsade announced to BBC News that his militia would eject the TFG by force if they did not withdraw from the city. According to Professor Robert Pape of the University of Chicago, the decision to invite Ethiopian troops to invade Somalia created an ideal trigger for extremists to carry out Somalia's first ever suicide attack, as the deployment of foreign troops loyal to the Christian-dominated government in Ethiopia was viewed by the majority of ordinary Somali citizens as a threat to the nations sovereignty.

The first clash between ICU and ENDF forces occurred on 9 October 2006. TFG forces, backed by the Ethiopian troops, attacked the ICU positions at the town of Burhakaba, forcing the courts to retreat. AFP reported that residents in Baidoa had witnessed a large column of at least 72 armed ENDF vehicles and troops transports depart from city. The ICU claimed that the ENDF had also sent another large deployment across the Somali border. Following the battle, Sharif Sheikh Ahmed announced "This is clear aggression...Our forces will face them soon if they do not retreat from Somali territories" and declared Jihad against Ethiopian military forces. Meles Zenawis government denied that ENDF troops were in Somalia, but local residents in Burhakaba confirmed their presence. The Economist reported that the Ethiopian military incursion had set off a fierce reaction even among the most moderate of the ICU, and a recruitment mobilization began in order to raise a force to take back Burhakaba.

During early November 2006, Puntland government officials threatened to "either incarcerate, kill or deport" religious leaders who formed an Islamic Court in the city of Galkayo. Several weeks later after intense local pressure, Puntland declared it would move towards adopting Sharia following a meeting between committee of religious heads and leader of the state, Mohamud Muse Hersi. High ranking Somaliland military officers defected to the ICU. Islamic Courts officials reported around 100 fighters from Puntland had defected to join their ranks in mid-November. On 29 November 2006, the courts claimed Ethiopian forces had shelled Bandiradley. The next day ICU forces ambushed an ENDF convoy outside of Baidoa.

Full scale invasion
In late December 2006, approximately 50,000 Ethiopian troops backed by tanks, Mi-24 helicopter gunships and Su-27s launch a full scale invasion into Somalia to topple the ICU and install the TFG. Alongside these troops, the Bush Administration covertly deployed US Special Forces backed by AC-130 gunships in support of ENDF forces. The lightly armed court forces were unable to counter ENDF/US air supremacy and armour. The timing and scale of the attack surprised many international observers, leading many to conclude that it was 'fairly obvious that Ethiopia had received significant help' during the invasion. Reuters reported American and British Special Forces, along with US-hired mercenaries, had been laying the ground work for the invasion within and outside Somalia since late 2005. During the invasion the United States provided satellite surveillance of ICU forces to the ENDF, along with extensive military and logistical support extending to the provision of spare parts. The European Union was reportedly 'exceptionally unhappy' about the heavy US support for the invasion, and held back funds for the newly created AMISOM mission for several months.

To avoid turning Mogadishu into a war zone once again, the ICU withdrew from the city on December 26, 2006. The top leaders of the Islamic Courts Union, including Sheikh Hassan Dahir Aweys, Sheikh Sharif Sheikh Ahmed and Sheikh Abdirahman Janaqow, resigned the next day.

Insurgency (2007–2009)
In the last days of December 2006, Ethiopian and TFG troops entered Mogadishu. Following the Ethiopian invasion and subsequent occupation, Somalia once again began slipping into a state of chaos. Between 2007 and 2008 approximately two-thirds of Mogadishu's residents were forced to flee the growing violence in the city, and Somalia began to experience one of the worst humanitarian crises in its history. Despite the general collapse of the organization in early 2007, members of the Islamic Courts Union regrouped and continued fighting against the Ethiopian occupation during 2007 and 2008. The Ethiopian government accused ICU fighters of fighting alongside the ONLF during the April 2007 Abole raid. By November 2008, ICU insurgents controlled the cities of Jowhar and Beledweyne. These regions operated independently of Al-Shabaab and the two groups came into contention. Al-Shabaab spokesman Mukhtar Robow publicly denied conflict between the two groups and claimed that although there had been past differences, both factions cooperated on the grounds opposing an Ethiopian military presence.

In January 2009, fighters who claimed loyalty to Islamic Courts Union engaged in a large military confrontation in Balad, Middle Shabeelle, against Al-Shabaab resulting in several deaths. Al-Shabaab put out a statement announcing that it was 'saddened' by the hostilities.

Post–ICU rule
In the wake of the ICU's disintegration, fringe Islamic groups began empowering themselves as Somalis from many walks of life rallied against the Ethiopian invasion and violence greatly escalated over the following years. Al-Shabaab, an obscure organization at this point, gained immense popularity as a resistance group fighting against the Ethiopians. Consequently, much of Somalia south of Mogadishu became Al Shabaab ruled territory. The Islamic Courts Union had actively fought pirate activity on the Somali coast, and consequently piracy thrived in their wake.

"Under the Courts, there was literally no piracy."During the period the of Courts governance, the number of militia road checkpoints in Somalia (along with the cost of passing them) drastically fell. After the invasion, militia checkpoints once again proliferated in large parts of southern Somalia in early 2007. The locations of these checkpoints on the road from Kismayo to Dhobley have remained relatively the same as of late 2023.

Creation of the ARS party and merger with TFG
In September 2007 the successor to the Islamic Courts Union, the Alliance for the Re-Liberation of Somalia (ARS), was founded by numerous high ranking ICU officials who had south refuge in Eritrea. Sheikh Sharif Ahmed was elected head of the organization and promptly declared war on Ethiopian forces. The ARS further announced its refusal to hold talks with the TFG until an Ethiopian withdrawal. In June 2008 the ARS and TFG signed a peace accord agreeing to the cessation of all hostilities between the two parties. Though successful, the talks were once again threatened by the issue of Ethiopian military forces deployed in Somalia.

Criticism and allegations
There was serious ideological friction between the ‘moderate’ wing of the Islamic Courts led by the Chairman of the Islamic Courts’ "Executive Council", Sheikh Sharif, and the "radical" wing led by the Chairman of the Courts’ Shura (Consultative or Legislative Council), Sheikh Aweys. These ideological divisions became clear when various wings of the Islamic Courts started making policies and statements without reference to the collective leadership. Many of them – mostly "radically" conservative social policies – were not popular among the wider population. Somalia's only popular drug, Khat, was outright banned. During the civil war many Somalis had relied the selling and distribution of the drug as one of their sole sources of income and consequently the ban had serious repercussions on people's ability to afford basic necessities. Charcoal exports were banned, on account of the industry devastating Somalia's fragile environment. Once again many Somalis had relied on the practice to make ends meet. Many Somali citizens had criticized the early Islamic courts for handing punishments out to petty criminals far more frequently than powerful gangsters and warlords. Radical elements in ICU, who viewed the TFG as an Ethiopian puppet, reportedly engaged in assassinations of TFG personnel. A United Nations monitoring group claimed the courts had sent 700 troops to fight alongside Hezbollah during the 2006 Lebanon War, though this claim has been held in question by many observers and analysts.

The ICU was accused of enacting extremist policies such as banning television, shutting down cinemas and preventing women from working. A Congressional Research Service report on Somalia investigating the allegations found no evidence to support to the assertion that women had ever been banned from working by the Islamic Courts. It was further revealed in interviews with local residents and courts officials that there had been some prohibitions on watching soccer games on television late at night, but merely due to disturbances and fighting. Cinemas had also been restricted, though only in the mornings at the direct request of Mogadishu parents who were frustrated with the issue of children skipping school to see films.