In 2016, terrorists used under-governed areas in northern, central, and southern Somalia as safe havens from where they conducted, planned, and facilitated operations with little resistance. Despite having made significant progress toward formally federating its member states in the latter part of 2016, Somalia continued to struggle with the provision of security, justice, and governance capacity at all levels needed to limit terrorists' freedom of movement, access to resources, and capacity to operate. Despite these limitations, all levels of Somali government continued to cooperate with U.S. counterterrorism efforts.

Al-Shabaab's ability to retain its safe haven in southern Somalia and regain new territory in central Somalia was due largely to lapses in offensive counterterrorism operations during 2016. The group carried out a series of complex assaults and raids against the African Union Mission in Somalia (AMISOM) forward-operating bases that resulted in the deaths of hundreds of AMISOM and Somali soldiers, the deadliest of these occurred in January against a Kenyan forward-operating base in the Gedo region town of Ceel Adde.

Although select U.S.-trained Somali forces made limited progress against al-Shabaab in 2016, the Somali National Army, as a whole, remained incapable of securing and retaking towns from al-Shabaab independently. In the latter part of 2016, Ethiopian forces largely withdrew from some areas it controlled in central Somalia, leaving previously liberated towns in Bakool, Hiiraan, and other regions, vulnerable to al-Shabaab.

In northern Somalia, a small group of former al-Shabaab members who had aligned with ISIS in October 2015 established a presence in remote areas that provided access to rudimentary ports along the coast of the Gulf of Aden and proximity to the Arabian Peninsula. Less than a year after pledging allegiance to ISIS, the group established a safe haven in the Golis Mountains of Puntland and temporarily took the port town of Qandala, which was retaken by Puntland's security forces in December 2016. The ISIS-aligned faction retreated to the mountains where a group of roughly 200 fighters remained out of the reach of regional security forces.

As seen in previous years, al-Shabaab kept much of its safe haven in the Jubba River Valley as a primary base of operations for plotting and launching attacks throughout Somalia and northern Kenya. The group's operatives controlled several villages and towns throughout Jubaland region, including Janaale, Jilib, and Kunyo Barow, and exploited the porous border regions further south between Kenya and Somalia to launch cross-border attacks.

Following one of the deadliest terrorist attacks in its history in April 2015 in Garissa, Kenya, increased its security presence along its northeastern border with Somalia to detect and counter al-Shabaab's cross-border operations, especially in and around the Boni Forest area. During 2016, al-Shabaab capitalized on Kenya's limited border security capacities by conducting smaller-scale attacks against soft targets and law enforcement facilities in Mandera and other northeastern counties in Kenya. The group continued to extort money from locals via illegal checkpoints and local businesses, while also taxing livestock and commodities, such as sugar, to finance its operations and pay recruits.

Despite chronically low capacity and human capital, the Federal Government of Somalia remained committed to regional counterterrorism efforts to eliminate al-Shabaab's access to safe haven in Somalia. Still heavily dependent on regional and international partners, Somalia progressed politically and took steps toward advancing its national security objectives through law enforcement and criminal justice reform in its urban areas.

According to independent sources and non-governmental organizations engaged in demining activities on the ground, there was little cause for concern for the presence of weapons of mass destruction in Somalia.

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