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In this paper, we demonstrate how multi-agent simulations of gender and sexuality-based marginalization can help us understand queer and trans experiences as complex, emergent, multi-level phenomena, which involve dynamic interactions between individuals, groups and institutions. We present illustrative cases that show how participants interacted with a multi-agent simulation of gender and sexuality-based marginalization and resilience. The participants used multi-level reasoning to make sense of the individual audio stories embedded in the simulation as well as the macro-level, emergent interactions between individuals (boids) and between individuals and institutions that were visualized in the simulation.