Joint Special Operations Task Force - Juniper Shield (JSOTF-JS)
Joint Special Operations Task Force - Trans Sahara (JSOTF-TS)

As of 2018 about 1,300 US military personnel work in the Lake Chad Basin — Niger, Nigeria, Cameroon and Chad — to help strengthen local militaries and counter Boko Haram, al-Qaida, IS and other extremist groups.

Joint Special Operations Task Force - Juniper Shield (JSOTF-JS) is the focal point for Special Operations Command Africa (SOCAFRICA) operations in the Trans Sahara region of Africa, to include increasing bilateral and regional capacity in the region to defeat terrorist and extremist organizations, in support of Trans Sahara Counterterrorism Partnership (TSCTP) objectives.

At some point during 2013, Joint Special Operations Task Force - Trans Sahara (JSOTF-TS) was redesignated as JSOTF-JS. Prior to that, the mission of Joint Special Operations Task Force - Trans Sahara (JSOTF-TS) had been to orchestrate all Deptartment of Defense efforts and activities toward accomplishing the Trans Sahara Counterterrorism Partnership (TSCTP) objectives, which included increasing bilateral and regional capacity in the region to defeat terrorist and extremist organizations, as part of Operation Enduring Freedom - Trans Sahara (OEF-TS).

Initiated in late 2006 by a handful of Special Operations officers, JSOTF-TS was created as a unique organization capable of orchestrating counter-terrorism objectives under the auspices of the US State Department initiated and led Trans-Sahara Counterterrorism Initiative (TSCTI) with its integrated 3-dimensional strategy of diplomacy, development and defense.

JSOTF-TS was transferred to US Africa Command (AFRICOM) from US European Command (EUCOM) in October 2008 and then subsequently was named a subordinate unit of Special Operations Command Africa (SOCAFRICA) in May 2009. The TSCTI was also transferred to AFRICOM and was eventually renamed the Trans Sahara Counterterrorism Partnership (TSCTP). Throughout the transition, the relatively small staff of about 40 uniformed personnel and civilians continued planning, coordinating and executing the full-spectrum of OEF-TS programs in the Trans-Saharan region. This included managing more than 30 US SOF-conducted military training engagements annually designed to enhance the counter-terrorism skills of pre-designated units and nearly 30 medical and about 15 veterinary civic action programs synchronized by its Civil Military Support Element in conjunction with local and national health authorities and non-governmental organizations.

The JSOTF-TS was also planning, managing and disbursing organizational equipment and vehicles to equip indigenous units in their security functions and developing as well as overseeing the JSOTF-TS created Trans-Sahara Security Symposium, an African taught week-long academic civil-military cooperation national and regional-focused forum targeted for African military and civilian representatives. Additionally, JSOTF-TS assumed the monumental task of planning, coordinating and executing the multi-national special operations forces Exercise Flintlock, which evolved as AFRICOM's premier special operations forces exercise on the continent.

On 8 April 2013, US Transportation Command (TRANSCOM) announced a solicitation for Trans-Sahara Short Take-Off and Landing (STOL) Airlift and Casualty Evacuation (CASEVAC) Support, in support of SOCAFRICA and JSTOF-TS operations. The spoliation was for a contractor to provide STOL aircraft support for CASEVAC, personnel airlift, cargo airlift, and air drop service in the Trans-Sahara region. The principal place of performance for the contract was defined as the Primary Operating Area, as dictated by operational requirements. Services would be based at Ouagadougou, Burkina Faso with JSOTF-TS's Joint Special Operations Aviation Detachment (JSOAD) and be capable of conducting operations from various temporary forward operating locations, to include primitive field accommodations, such as tents. The Primary Operating Area included, but was not limited to, the recognized political boundaries of Algeria, Burkina Faso, Cameroon, Central African Republic, Chad, Democratic Republic of the Congo, Ethiopia, Kenya, Libya, Mali, Mauritania, Morocco, Niger, Nigeria, Senegal, Sudan, South Sudan, Tunisia, and Uganda, as dictated by operational requirements. It was anticipated the most likely locations for missions from the above list would be to: Algeria, Burkina Faso, Cameroon, Chad, Libya, Mali, Mauritania, Morocco, Niger, Nigeria, Senegal, and Tunisia. In response to contractor questions, TRANSCOM later indicated that this support have previously been provided through the Department of Defense's Counter Narcoterrorism Program Office (CNTPO). It was later revealed that U.S. Training Center Inc. was the holder of the prior contract. On 25 July 2013, the contract, totaling almost $50 million, was awarded to Berry Aviation of San Marcos, Texas.

Pentagon and Nigerien defense officials said Islamic State fighters ambushed their forces 04 October 2017, killing four American soldiers, four Nigerien soldiers and a Nigerien interpreter. In the attack, a group of 12 members of a U.S. Special Operations Task Force had accompanied 30 Nigerian forces on a reconnaissance mission from the capital city of Niamey to an area near Tongo Tongo. Members of the team had just completed a meeting with local leaders and were walking back to their vehicles when they were attacked.

The New York Times reported 10 February 2018 that a draft military investigation into the deaths of US soldiers in Niger in 2017 called for the Pentagon to reduce the number of ground missions in West Africa. Military officials with knowledge of the findings told the newspaper the investigation also concluded that commanders in the field should have less authority to send troops on potentially high-risk patrols. Higher-level commanders would now need to approve certain missions that carry a higher risk. The officials said US troops would continue to carry out joint patrols with local military forces, but say military officials will more thoroughly vet such missions. The officials said missions would not be scaled back in Libya or Somalia, where US troops had been working with local forces to fight Islamic State and al-Shabab militants.