In November 2016, Uganda’s armed forces raided the Rwenzururu kingdom palace in Kasese Municipality, arresting and detaining the king and other kingdom officials on treason and other charges. This was the climax to a puzzling wave of violence that was then unfolding in the Rwenzori Region. We consider this violence an unintended consequence of the deepening politics of fragmentation, which takes two forms: “kingdomization” and “districtization.” Through fragmentation, Uganda’s ruling elites seek to weaken subnational concentrations of power, resources, and legitimacy wielded by otherwise coalesced, potentially strong, subnational authority structures and sociopolitical groups. Fragmentation fractures preexisting intra-regional unity, generates new conflicts, and reopens old wounds, leading to violent encounters at the sub-national level, between regional sub-groups, and with the central state. This unfolding of violent encounters involving both state and non-state actors has important ramifications for managing national security within socially fragile contexts and a politically fragmented polity.