Somalia Drifts Towards Disintegration as Political Leaders Squabble, the Army Fragments and Al-Shabaab Gains Ground

While Uganda is pressing Mogadishu to finalize an aviation agreement that could expand trade and regional connectivity, Somalia is sinking deeper into constitutional paralysis, political fragmentation and a military crisis.

MOGADISHU (WDN) – Uganda has urged Somalia to accelerate negotiations on a Bilateral Air Services Agreement (BASA), seeking a clear legal framework for Uganda Airlines to continue and expand its direct flights between Entebbe and Mogadishu.

The request, reported by Uganda’s Daily Monitor on November 10, comes at a particularly difficult moment for Somalia. While Kampala is concentrating on commercial aviation, trade and regional economic integration, Somalia’s political leadership remains consumed by a deepening election and constitutional dispute that threatens the cohesion of the federal state and undermines the country’s ability to confront Al-Shabaab.

The contrast is striking: Uganda is negotiating the practical arrangements of economic cooperation with Somalia, which its political institutions are increasingly struggling to perform their most fundamental responsibility maintaining basic service and national stability.

Uganda pursues economic opportunities as Somalia’s crisis deepens

Uganda’s Permanent Secretary in the Ministry of Foreign Affairs, Vincent Bagiire Waiswa, has called for the swift conclusion of the aviation agreement, confirming that Kampala is ready to sign once the outstanding legal review is completed.

Uganda Airlines currently operates four weekly direct flights between Entebbe and Mogadishu. Kampala says the airline faces operational difficulties in Somalia and wants the agreement to establish clear rules governing its commercial activities.

Somalia, meanwhile, wants reciprocal arrangements that would allow its own airlines to operate flights to Uganda. The agreement would regulate designated airlines, flight frequencies, airport charges, aviation taxes and safety requirements.

President Hassan and President Musevani

Uganda also sees Somalia as a potential commercial gateway through which its landlocked economy could reach markets in the Gulf. Both governments are targeting December 2026 for the agreement’s signing, following legal review.

These are legitimate economic ambitions. Yet they expose a troubling contradiction: international partners are pursuing long-term commercial arrangements with Somalia while its domestic political settlement remains increasingly uncertain.

A constitutional dispute consuming the state

Somalia’s political crisis is no longer simply a disagreement over who should govern or which electoral model should be adopted. It has developed into a confrontation over constitutional authority, the legitimacy of political institutions and the future of the federal system.

The Associated Press reported that Somalia’s Supreme Court ruled that President Hassan Sheikh Mohamud’s mandate had expired, rejecting the argument that constitutional amendments permitted him to remain in office until 2027. The court also directed political leaders to agree on an electoral arrangement within 30 days and elections to be held within 90 days.

Meanwhile, disagreements between Mogadishu, Puntland, Jubaland and opposition groups have left the country without a broadly accepted electoral settlement.

The November assessment by the Security Council Report similarly highlights unresolved disputes over constitutional amendments, presidential term extensions and regional electoral arrangements.

The consequences extend beyond political negotiations. When national leaders cannot agree on the constitutional rules governing the state, government institutions become vulnerable to competing political loyalties, while national priorities are subordinated to struggles for power.

The national army is becoming another casualty

Perhaps the most alarming development is the growing vulnerability of Somalia’s national army to political interference and clan mobilisation.

The national armed forces were established to defend the country, protect its citizens and uphold the constitutional order. They were never intended to become instruments for settling political disputes, enforcing the ambitions of an incumbent administration or serving competing clan interests.

Yet the distinction between national military service and clan allegiance is becoming increasingly blurred.

Recent reports from Hiiraan are particularly disturbing. According to Somali Guardian’s November 10 report , soldiers from the Hawadle clan serving in the Somali National Army abandoned their positions and returned to Beledweyne following a call from their traditional leader, Ugas Yusuf Ugas Hassan.

The report described groups of soldiers arriving at the traditional leader’s residence, raising concerns about the federal command’s ability to maintain military discipline and national cohesion.

This is more than a local security dispute. It exposes the fragility of an army whose personnel may respond to clan authorities rather than the national chain of command.

The danger is compounded when senior security institutions are drawn into political negotiations while the military itself struggles to maintain a unified command structure.

A national army cannot function effectively if soldiers are mobilised according to clan instructions, deployed according to political calculations or withdrawn from frontlines because of disputes with the federal leadership.

Al-Shabaab stands to benefit from the fragmentation

The greatest beneficiary of Somalia’s political and military disintegration may be Al-Shabaab.

The insurgent organisation does not need to defeat a cohesive national army in a conventional confrontation if political divisions, military defections and competing regional loyalties continue to weaken the government’s ability to coordinate its forces.

Every abandoned frontline, every breakdown in military command and every dispute that prevents cooperation between federal and regional authorities creates opportunities for the insurgents.

The Associated Press has reported that Al-Shabaab continues to control extensive rural areas and conduct attacks in Mogadishu and other cities. The withdrawal and redeployment of international forces also create additional uncertainty over who will secure strategically important positions.

The danger is therefore not merely that Al-Shabaab could regain territory previously recovered by government forces. It is that the organisation could exploit a progressively fragmented state whose political leaders are unable to establish a common security strategy.

Somalia’s military achievements cannot be sustained through fragmented command structures, politically motivated deployments and clan-based mobilisation. Counterterrorism requires national coordination, reliable financing, professional discipline and cooperation between federal and regional administrations.

A country cannot fight an insurgency while dismantling its own institutions

The fundamental contradiction facing Somalia is increasingly difficult to ignore. The government needs a unified national army to confront Al-Shabaab, yet the political environment is undermining the very cohesion on which that army depends.

The presidency and opposition must recognise that the constitutional dispute is no longer confined to political elites. Its consequences are reaching military barracks, regional administrations and communities living in areas threatened by insurgent expansion.

Somalia cannot afford to turn its national armed forces into instruments of political competition while allowing clan loyalties to replace national military discipline.

Uganda’s pursuit of an aviation agreement is a reminder that international relations and economic development require functioning institutions, predictable rules and political stability. Somalia needs those same foundations urgently.

The danger is that while Somalia’s political leaders continue arguing over who controls the state, Al-Shabaab may steadily acquire the space, territory and strategic advantage needed to challenge what remains of it.

A country cannot defeat an insurgency by weakening its own army, nor can it preserve federal unity through political confrontation and constitutional uncertainty. Unless Somalia’s leaders urgently restore political consensus, military professionalism and cooperation between federal and regional authorities, the country’s already fragile statehood will face an even greater threat of fragmentation.

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