The collapse of the August 2015 Agreement on the Resolution of the Conflict in the Republic of South Sudan (ARCSS) highlights a broader puzzle in conflict resolution: why mediated agreements in protracted civil wars so often unravel during implementation. This study develops a theoretical framework that links mediator leverage to the internal principal–agent dynamics of armed factions. Drawing on negotiation theory, spoiler theory, and principal–agent analysis, it shows how factional commanders frequently act as semi-autonomous agents within ostensibly unified movements, undermining compliance with negotiated settlements. Based on detailed process tracing of the IGAD-led mediation (2014–2018) and comparative analysis with the Lusaka Protocol (1994) and the Accra Agreement (2003), the findings indicate that externally brokered agreements are especially vulnerable when internal chains of command remain fragmented. Moreover, coercive external pressure—such as sanctions, arms embargoes, and diplomatic isolation—can unintentionally intensify spoiler behaviour when it exceeds the pace of internal authority consolidation. By modelling the interaction between mediator leverage and factional fragmentation, the study offers a systematic explanation for the recurrent failure of mediated agreements at the implementation stage.