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This paper uncovers the evolution of cities and Islamist insurgencies, so called jihad, in the process of the reversal of fortune over the centuries. In West Africa, water access in ancient periods predicts the locations of the core cities of inland trade routes -- the trans-Saharan caravan routes -- founded up to the 1800s, when historical Islamic states played significant economic roles before European colonization. In contrast, ancient water access does not have a persistent influence on contemporary city formation and economic activities. After European colonization and the invention of modern trading technologies, along with the constant shrinking of water sources, landlocked pre-colonial core cities contracted or became extinct. Employing an instrumental variable strategy, we show that these deserted locations have today been replaced by battlefields for jihadist organizations. We argue that the power relations between Islamic states and the European military during the 19th century colonial era shaped the persistence of jihadist ideology as a legacy of colonization. Investigations into religious ideology related to jihadism, using individual-level surveys from Muslims, support this mechanism. Moreover, the concentration of jihadist violence in "past-core-and-present-periphery" areas in West Africa is consistent with a global-scale phenomenon. Finally, spillovers of violent events beyond these stylized locations are partly explained by organizational heterogeneity among competing factions (Al Qaeda and the Islamic State) over time.