This article examines the structure and spatial patterns of violent political organizations in the Sahel-Sahara, a region characterized by growing political instability over the last 20 years. Drawing on a public collection of disaggregated data, the article uses network science to represent alliances and conflicts of 179 organizations that were involved in violent events between 1997 and 2014. To this end, we combine two spectral embedding techniques that have previously been considered separately: one for directed graphs (relationships are asymmetric), and one for signed graphs (relationships are positive or negative). Our result show that groups that are net attackers are indistinguishable at the level of their individual behavior, but clearly separate into pro- and anti-political violence based on the groups to which they are close. The second part of the article maps a series of 389 events related to nine Trans-Saharan Islamist groups between 2004 and 2014. Spatial analysis suggests that cross-border movement has intensified following the establishment of military bases by AQIM in Mali but reveals no evidence of a border sanctuary. Owing to the transnational nature of conflict, the article shows that national management strategies and foreign military interventions have profoundly affected the movement of Islamist groups.