Africa File

The Africa File is an analysis and assessment of the Salafi-jihadi movement in Africa and related security and political dynamics. 

Africa File: Libya will fragment further as strongman loses support

[Notice: The Critical Threats Project frequently cites sources from foreign domains. All such links are identified with an asterisk (*) for the reader's awareness.]

Libya will fragment further as strongman Khalifa Haftar loses support. Turkish military support for forces aligned with the UN-backed government in Tripoli delivered a potentially decisive blow to Haftar’s yearlong campaign to seize Libya’s capital on May 18. Haftar’s domestic coalition is weakening and his primary foreign backers (the UAE, Egypt, and Russia) must decide whether to prop up his failing campaign. A renewed campaign for Tripoli could likely bring violence on a scale that Libya has not yet seen as external players pour military resources into the conflict. But even if this case is averted, the freezing or ending of the Tripoli campaign is unlikely to stabilize the country. Anti-Haftar players around Tripoli will likely return to fighting each other in the absence of an external foe. In the east, Haftar’s military rule could disintegrate and yield a war-within-a-war.

Libya’s crisis has regional and global implications. The foreign players that are fueling Libya’s war are pursuing disruptive goals; Russia’s involvement in Libya is part of its effort to pressure Europe and challenge NATO, and the Middle Eastern states acting in Libya are engaged in a power struggle that is destabilizing much of the Middle East and Africa. The ongoing war and collapse of the state are setting conditions for Salafi-jihadi groups such as the Islamic State and al Qaeda to recover in Libya and again gain a strategic haven on the Mediterranean coast.

Unfortunately, Libya’s is far from the only crisis that is benefiting or will likely benefit the Salafi-jihadi movement in Africa. The COVID-19 pandemic and accompanying economic crisis are putting unprecedented strain on many African states; governance will worsen in many cases, and the likelihood of instability and state collapse is rising. Such collapses could destabilize regions and would fuel conflict and extremism, as Critical Threats Project Research Manager Emily Estelle argues in a forecast of the effects of the COVID-19 pandemic on the Salafi-jihadi movement in Africa.

Read Further On:

North Africa
West Africa
East Africa

Recent Critical Threats Project Publications:

Forecast: The African Salafi-Jihadi Movement After COVID-19” by Emily Estelle

Eyes on the Other Global Crises” by Emily Estelle (Originally published in RealClearWorld)

Salafi-Jihadi Ecosystem in the Sahel” and interactive graphic by Katherine Zimmerman

At a Glance: the Salafi-jihadi Threat in Africa

Updated April 28, 2020

The COVID-19 pandemic will hasten the reduction of global counterterrorism efforts, which had already been rapidly receding as the US shifted its strategic focus to competition with Iran, China, Russia, and North Korea. The US administration has begun to withdraw troops from Afghanistan after signing a peace deal with the Taliban on February 29. The future of US forces in Iraq and Syria is uncertain following the destruction of the Islamic State’s physical caliphate and its leader’s death, though the group already shows signs of recovery. The US Department of Defense is also considering a significant drawdown of US forces engaged in counterterrorism missions in Africa, though support for the French counterterrorism mission in the Sahel has been extended for now.

This is happening as the Salafi-jihadi movement, including al Qaeda and Islamic State affiliates and allies, continues to make gains in Africa, including in areas where previous counterterrorism efforts had significantly reduced Salafi-jihadi groups’ capabilities. The movement was already positioned to take advantage of the expected general reduction in counterterrorism pressure before the pandemic hit; now, a likely wave of instability and governmental legitimacy crises will create more opportunities for Salafi-jihadi groups to establish new support zones, consolidate old ones, increase attack capabilities, and expand to new areas of operations.

The Salafi-jihadi movement is on the offensive in Burkina Faso, Niger, and Mali, where it has pressured the Malian government to offer negotiations. It is also stalemated in Somalia and Nigeria and persisting amid the war in Libya. Conditions in these last three countries favor the Salafi-jihadi movement rather than its opponents in the coming year.

Libya’s civil war, reignited on a large scale in April 2019, will continue to fuel the conditions of a Salafi-jihadi comeback, particularly as foreign actors prolong and heighten the conflict. Counterterrorism efforts in Somalia and Mali rest on the continued efforts of international coalitions, support for which is eroding in both host and troop-contributing countries and on local partners that have demonstrated their inability to govern effectively or establish legitimacy in their people’s eyes.

Amid these conditions, US Africa Command (AFRICOM) is shifting its prioritization from the counterterrorism mission to great-power competition, a move also intended to reduce risk after a 2017 attack killed four servicemen in Niger. US and European powers aim to turn over counterterrorism responsibilities to regional forces of limited effectiveness—such as the G5 Sahel, which is plagued by funding issues, and the African Union Mission in Somalia, which is beginning a scheduled drawdown. COVID-19 has exacerbated existing problems with these forces, with contributing nations reevaluating their commitments to foreign intervention during the pandemic.

The Salafi-jihadi movement has several main centers of activity in Africa: Libya, Mali and its environs, the Lake Chad Basin, the Horn of Africa, and now northern Mozambique. These epicenters are networked, allowing recruits, funding, and expertise to flow among them. The rise of the Salafi-jihadi movement in these and any other places is tied to the circumstances of Sunni Muslim populations. The movement takes root when Salafi-jihadi groups can forge ties to vulnerable populations facing existential crises such as civil war, communal violence, or state neglect or abuse (all now likely to be exacerbated by the pandemic). Local crises are the incubators for the Salafi-jihadi movement and can become the bases for future attacks against the US and its allies.




North Africa


Libyan warlord Khalifa Haftar may lose support after his forces suffered a major setback in the campaign to seize Libya’s capital. Haftar’s forces, backed by the UAE, Russia, and Egypt, have been attempting to seize Tripoli since April 2019. Forces aligned with the UN-backed Government of National Accord (GNA) have fended off Haftar’s advance for the past year with increasing support from Turkey. Turkish air support proved decisive on May 19, when GNA-aligned forces seized Wattiya Airbase in northwestern Libya from the Haftar’s Libyan National Army (LNA) after weeks of airstrikes.

The LNA’s loss of Wattiya is a major military setback. The base, controlled by LNA-aligned forces since 2014, was the LNA’s only such position in northwestern Libya; its nearest airbase is now at Jufra in the center of the country. GNA-aligned forces seized an advanced Russian-made air-defense system (likely supplied by the UAE) and destroyed several others while taking the base.  The conclusion of the Wattiya campaign will also allow GNA-aligned forces and Turkish drones to turn their focus to other fronts; they will likely move next to sever the LNA supply line to Tarhouna, the LNA’s remaining stronghold on the outskirts of Tripoli. LNA forces withdrew from the Tripoli frontline the following day, citing the last few days of Ramadan. This reposition likely seeks to avoid further immediate losses and prepare for a counterattack. Recent military buildup inside Libya could supply the firepower for a renewed LNA offensive; alternately, further GNA advance could degrade support for the LNA in Tripoli. The loss of Tarhouna would likely end the LNA’s Tripoli campaign entirely. The fate of the campaign depends on if and how Haftar’s backers choose to muster support. 

This setback comes as Haftar’s support base in eastern Libya fragments. Haftar declared military rule in eastern Libya in April 27 in an attempt to consolidate his power following prior losses. This declaration was also meant to reinforce Haftar’s position against a rival within the eastern Libyan bloc, House of Representatives Speaker Ageela Saleh. Saleh revealed on April 30 that he has been pursuing a political initiative to end the conflict with Russian support. Haftar’s declaration appears to have emboldened Saleh and turned some other allies against the general, including a prominent Salafi militia commander.

Haftar’s foreign backers must respond if they want to preserve the Tripoli campaign and prevent the disintegration of Haftar’s coalition. This comes as they are already reconsidering support for the field marshal, who promised a quick victory in the Tripoli campaign that has now stretched on for 13 months. Russia’s foreign minister criticized Haftar’s April 27 announcement, reflecting growing frustration with Haftar’s ineffectiveness unwillingness to take cues from Moscow. Egypt, concerned about the security of its western border, may also be seeking alternatives to Haftar. And the UAE, which has been Haftar’s staunchest supporter even since his April 27 power grab, has called for a ceasefire and may also seek a new partner if it becomes clear that Haftar can neither seize Tripoli nor hold the east no matter his level of external support.

Forecast: Libya will continue to fragment on any of several likely trajectories.

  • GNA-aligned forces may continue their advance as Haftar’s coalition crumbles. This outcome could spawn smaller wars in the east, which will devolve into economic crisis and attempts to control LNA-captured institutions, and in the west, where LNA-aligned parties will need to either surrender or fight and intra-militia tensions will reemerge in the absence of an external foe.
  • Haftar’s backers may provide sufficient support to preserve his position temporarily and return the Tripoli fight to a stalemate, potentially in preparation for a renewed offensive (particularly if Turkish assets are drawn elsewhere). But such support is unlikely to heal rifts in the east in the long term nor increase Haftar’s chances of taking over the entire country.
  • Haftar’s backers may seek to replace him and empower alternate authorities in the east, under parliamentary speaker Ageela Salah. These newly empowered eastern leaders may attempt to strike a deal with the GNA, though it is not clear that their demands (or the UAE’s) will be sufficiently less maximalist than Haftar’s. Conflict would decrease in the short term and the current war may even end. Spoilers not represented by these factions will likely pursue their interests by force, however, so a negotiated settlement would likely falter within its first year.

All these most likely outcomes preserve and worsen the conditions that allow Salafi-jihadi groups to strengthen. (Updated May 20, 2020)


West Africa


The Western Sahel

Jama’at Nusrat al Islam wa al Muslimeen (JNIM), the al Qaeda in the Islamic Maghreb affiliate in the Sahel, is waging a Ramadan campaign titled “Invasions of the Holy Month” targeting local and international security forces in Burkina Faso, Mali, and Niger. The “Invasions of the Holy Month” campaign, which was announced on May 4, has included frequent IED attacks and a multi-part *attack on Malian Army positions in central Mali’s Mopti region on April 28.[1] The campaign has not included a significant inflection in JNIM’s activity or capabilities but reflects a coordinated messaging strategy. JNIM’s recent messaging has also incorporated the COVID-19 pandemic as part of an ongoing effort to turn public opinion against the French intervention in Mali. JNIM has called for the withdrawal of French forces as a precondition for negotiations with the Malian government.

JNIM’s messaging is likely most effective when it echoes acute popular grievances, including security force abuses against Fulani and Tuareg populations. JNIM claims attacks on security forces as revenge for attacks on civilians. Such abuses have spiked in northern Burkina Faso in the past two months. Burkinabe security forces allegedly executed 31 detainees in northern Burkina Faso on April 9. JNIM claimed an ambush of Burkinabe forces in Banwa Province near the Malian border on May 18 as revenge for the Burkinabe forces’ alleged persecution of Muslim in a nearby town.[2] Further human rights abuses will legitimate Salafi-jihadi claims to provide a viable alternative to flawed states.

Tensions remain high between the Islamic State in the Greater Sahara (ISGS) and JNIM. An Islamic State newsletter accused JNIM of attacking its fighters in the Sahel and criticized JNIM’s willingness to negotiate with the Malian government in early May. JNIM and ISGS have clashed across several regions of Mali following a March 12 incident that killed an ISGS leader. Clashes have decreased since mid-April, though this may be because ISGS came under increased pressure from the French counterterrorism mission in the Sahel earlier in the month. Unconfirmed reports on jihadi forums claim that ISGS has sought to reduce tensions but JNIM has rejected this outreach.[3]

ISGS and JNIM have cooperated in the past but also clash over territory, economic opportunities, and personnel. The current clashes are the most severe and sustained eruption of hostilities between the groups.

Forecast: The perceived illegitimacy of the Malian elections will fuel unrest with interest groups in northern Mali, possibly distracting the state from counter-Salafi-jihadi efforts and creating more opportunities for Salafi-jihadi groups to establish mutually beneficial agreements with other anti-government groups. Salafi-jihadi groups will begin to establish governing institutions—such as courts—in the Burkinabe-Malian-Nigerien tri-border area in the next six months, though it may mask these efforts to facilitate a deal with the Malian government.

Salafi-jihadi groups may also work through local governance structures to present themselves as legitimate interlocutors and avoid scrutiny. Attacks on Fulani civilians will drive greater popular support to JNIM, which will present itself as a more moderate alternative.

The JNIM-ISGS clashes will likely not have a significant operational effect because French pressure on ISGS is already limiting the group’s operations in the near term. ISGS’s opposition to negotiations may increase JNIM’s palatability to local populations over time. (Updated May 20, 2020)




East Africa


Al Shabaab is adapting its COVID-19 response as the outbreak worsens in Somalia. The outbreak provides an opportunity for al Shabaab to provide services and bolster its reputation as an alternative to the Somali Federal Government (SFG), though the group also risks backlash should its response appear to worsen the outbreak. Al Shabaab’s initial response to COVID-19 focused on blaming the outbreak on the presence of foreign forces and criticizing the SFG’s pandemic control measures, including mosque closures.[4] The group intensified its response in mid-May by appointing a committee to monitor the pandemic in al Shabaab-controlled territories and advise authorities. Al Shabaab also claimed that the virus has not reached areas under its control.[5]

Al Shabaab is increasing attacks targeting the African Union Mission in Somalia’s (AMISOM) Halane camp in Mogadishu after claiming that Somalia’s first COVID-19 case originated from the base. Al Shabaab’s spokesman also accused AMISOM and UN representatives of deliberately spreading the virus.[6] AMISOM had temporarily locked down Halane in April after a contractor tested positive for the coronavirus. Al Shabaab fired mortars at the base on *April 26 and May 4.[7]

COVID-19 may disrupt AMISOM operations inside Somalia. A Ugandan military official announced on May 2 that Ugandan AMISOM forces will *suspend rotations in Somalia to prevent the disease’s spread.

Forecast: Al Shabaab will attempt to capitalize on backlash to the SFG’s pandemic response to present itself as the more legitimate governing force in Somalia but may suffer its own delegitimization if its efforts—potentially including disrupting aid—are seen as causing harm in the areas it controls. The pandemic may reduce targets available for al Shabaab’s campaigns, potentially leading to fewer attacks (especially if the planned 2020 elections are postponed). The pandemic may also delay al Shabaab’s efforts to execute a spectacular attack in Kenya. (Updated April 14, 2020)

[1]“JNIM Announces “Invasions in the Holy Month,” Claims 3 Attacks on Enemy Forces in Mali and 1 in Burkina Faso,” SITE Intelligence Group, May 4, 2020, available by subscription at

[2] “JNIM Claims Killing 9 Burkinabe Soldiers in Ambush Following Alleged “Dirty Mission” by Army,” SITE Intelligence Group, May 19, 2020, available by subscription at

[3] “Jihadist Alleges JNIM Rejected IS’ Reconciliation Offer and Wounded Local Official,” SITE Intelligence Group, May 12, 2020, available by subscription at

[4] “Sermon Delivered In Somali Mosques in Shabaab-Controlled Areas Identifies Protective Measures Against Covid-19 While Decrying Mosque Closures,” SITE Intelligence Group, May 11, 2020, available by subscription at

[5] “Shabaab Appoints Committee To Monitor Covid-19 Pandemic in its Controlled Territories,” SITE Intelligence Group, May 13, 2020, available by subscription at

[6] “Shabaab Spokesman Suggests Foreign Forces Intentionally Spread Coronavirus in Somalia,” SITE Intelligence Group, April 28, 2020, available by subscription at

[7] “Shabaab Claims Shelling Halane Base Camp 2 Weeks After Last Strike, Allegedly Inflicting 14 Casualties,” SITE Intelligence Group, May 14, 2020, available by subscription at

View Citations
Arrow down red
May '20
Apr '20