This article examines the political and institutional processes through which conflict, displacement, and aid dependence have dismantled agricultural systems and rural livelihoods in South Sudan in South Sudan with comparative reference to Mozambique and Rwanda. It asks how politically produced agricultural collapse structures political order during successive war cycles from the liberation period to the present, combining agrarian political economy, food sovereignty theory, livelihoods analysis, and the conflict-agriculture nexus with a research design centred on longitudinal analysis of agricultural systems and food-security data, political economy fieldwork, interviews with farmers and officials, and comparison with post-conflict agricultural recovery elsewhere in Africa. The central argument is that the issue under study is not best explained as a discrete policy failure or a short-lived crisis. Rather, it is reproduced through linked institutional and political mechanisms that reshape incentives, authority, and access to resources over time (Bernstein, 2010; McMichael, 2013) (Scott, 1976; Chambers & Conway, 1992). Across the paper, the analysis tracks how these mechanisms operate in practice, what variation they generate, and why reform agendas that ignore the underlying political settlement rarely succeed. The article therefore contributes both a conceptual synthesis and a grounded comparative interpretation of the focal case. Its wider implication is that durable reform requires institutional redesign, political bargaining, and accountability strategies capable of reaching the real sites where power is exercised (DFID, 1999; FAO, 2023) (WFP, 2024; de Waal, 1997).