In 2025, security challenges are re-surfacing in the Horn of Africa, and this challenge in relation to countering terrorism requires regional counter-terrorism measures. In cases of Kenya and Somalia, the reemergence of al-Shabaab and the increased scope of operations of ISIS-Somalia has continued to challenge domestic stability. The July 2025 offensive by Al-Shabaab, the recapture of key grounds around Mogadishu, and tactical success of Al-Shabaab whose leaders claimed high-toll on casualties have reversed the progress of the last year thus throwing doubts of the long-lasting of international and national attempts.
Together with African Union Transition Mission in Somalia (ATMIS), Turkey and U.S. military advisors, the Somali government had recaptured more than 215 towns and villages as of the middle of 2025. However, al-Shabaab has since taken control of supply lines into towns such as Bulobarde disrupting transportation pathways as well as locking humanitarian aid. As ATMIS personnel increasingly work in a gradually more restricted environment, with exit strategies by AU forces being finalized, the pressure is piled upon the weak central government in Somalia and towards the regional allies.
Fragmented authority and Somalia’s internal disunity
The fissure between the central government in Mogadishu and autonomous regions like Puntland and Jubaland is one of the fundamental returning factors to the success of counterterrorism in Somalia. Such states still oppose centralization efforts towards the federal government on the basis that they have the right to take charge of their own security strategies. This loose style has enabled al-Shabaab to move around the administrative barrier, and use inter-regional loopholes to transfer human resources, raise funds, as well as to set up command centers.
This disintegration has also laid bare the weaknesses of Somali National Army operation which largely relies on external sources of funding and training thus proving vulnerable when foreign assistance wears thin. Although there are local military successes, the effort of achieving the coherent command structure complicates the intelligence fusion as well as joint operation.
Incomplete integration of international support
International partners such as the U.S and Turkey have continued to be active especially in making sporadic contributions but they are not systemic. The loop of implementation of high-tech equipment, the lack of consistent logistic pipelines, and poly-coordination of the Somali government and foreign missions have compromised the effectiveness of the long-term efficacy of the counterterrorist actions. With ATMIS set to fold its tent, the Somali government is yet to seal the vacuum of operation that will discourage the risk of terrorist groups consolidating their power in key corridors.
Kenya’s expanded role in regional counterterrorism
Kenya has enjoyed many attacks by al-Shabaab in the past decade and such tragic moments like the Westgate Mall attack in 2013 and the Garissa University attack in 2015 have defined the national security attitude of Kenya. By 2025, Kenya has taken a more proactive approach; more weight is given to cross-border intelligence gathering, preemptive projection of force and coalition-building as militant incursions are on the rise in areas around Mandera and Lamu counties.
Kenyan defense ministers have been quoted saying that regional cooperation is no longer a choice but rather it is a necessity. Nairobi, Kenya also hosted the 2025 African Chiefs of Defense Conference, a place where its status as a diplomatic and operational center to pursue multilateral security objectives was outlined. Major agenda points were maritime security, cyber security, and a synchronized aerial security to interdict jihadist supply chains and lines in Somalia and further to East Africa.
American and African Command partnerships
U.S. Africa Command (AFRICOM) is a key party in the security of Kenya. In the 2025 policies of General Michael Langley, AFRICOM still follows the strategy of African-led operations with American support. These are joint training, medevac operations on the battlefield and deployment of unmanned systems to track al-Shabaab activities in Somalia and northeast Kenya.
The partnership between the Kenya Defence Forces and the Massachusetts National Guard continues to evolve, reflecting a broader shift toward comprehensive force development rather than episodic intervention. Nairobi’s defense ministry sees these collaborations as critical not only for counterterrorism but also for preparing against environmental and humanitarian disruptions that are increasingly linked to regional instability.
Obstacles to sustaining counterterrorism gains
Between February and June 2025, the United States conducted 38 airstrikes in Somalia attacking high value al-Shabaab and ISIS-Somalia leaders. The problem with such kinetic operations, as Kenyan and Somali analysts warn, is that it only degrades command structures but fails to take any action on militant recruitment and community alienation roots. Unless there are corollaries of similar investments in governance, economic growth and rule-of-law systems, security gains will probably be short-lived.
The interest of Kenya as a whole is the economic corridor’s security and the fight in taking down the spread of extremism to the coastal and the inland provinces. The weakness of Somalia political institutions is impaired in regional planning and even though Nairobi is technologically advanced, it cannot completely shield this region against the contagion of a failing Somali security system.
Maritime and regional vulnerabilities
The Bab el-Mandeb Strait is a significant maritime chokepoint, located just north of the Somali coast among the most important ones in the whole world. Further Somalian instability further threatens formations of militants or blockage of shipping channels. In 2025 Kenyan naval strategists and foreign analysts have voiced concern over uncontrolled arms and drug trafficking between the Swahili coast, Somalia and Yemen.
With the decrease in the presence of AU troops, there is no more time to waste in coming up with a maritime solution that incorporates both local Somalia and regional powers. The offshore patrol vessels and drone surveillance program Kenya is investing in by 2025 will seek to address this gap, although there are still political suspicions and unstable finances making sustained cooperation between countries in the region a challenge.
Civil perspectives and digital narratives
Digital platforms continue to shape public perception and offer critique of state-led strategies. Pauline Njoroge, a respected Kenyan commentator, addressed the complexity of regional counterterrorism dynamics.
She noted that both Kenya and Somalia are “facing a test of political maturity and shared destiny,” emphasizing that military firepower alone cannot defeat a cross-border ideology.
The sentiments shared by Njoroge have been largely echoed by the policy circles and in the media who have demanded more community based methods, better governance and the need to recognize socio-economic factors that have driven radicalization. Her formulations make counterterrorism not only a military problem, but an issue that should be responded to on both the civilian, regional, and global levels.
A regional inflection point amid shared threats
Kenya and Somalia are at the tipping point. As al-Shabaab is changing its methods of operation, the gradual withdrawal of troops in the region, and internal political stability within Somalia is taking a downward turn, conventional counterterrorism models might no longer be applicable. Kenya has managed to play the role of stabilizing force through its military and diplomatic means which has increased its status widely but Nairobi cannot shoulder the success by itself.
Whether or not the gains achieved through partnership between the Africans and the West can be sustained will depend on how Somalia will rebuild their fragmented security structure, empower inclusive governance, and also strengthen federal and state initiatives. Concurrently, the need to gather regional players that Kenya has spearheaded presents an opportunity on which a more comprehensive strategy of security in the Horn of Africa can be established.
How/to what extent each country is able to transcend its domestic limitation and focus on collective security will determine the future of counter terrorism in East Africa. Depending on choices that are currently under discussion in Mogadishu, Nairobi, and the tactical capitals behind them, that chapter will either create a long-term peace or, once more, a pattern of re-escalation.
