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We present findings from a project about developing computational microworlds to teach middle schoolers about disease spread and prevention. The agent-based block-based computational microworld helps students model and test their ideas regarding how infectious diseases spread and how to prevent epidemics. The paper analyzes one student’s shift in thinking regarding COVID prevention strategies through building, testing, and debugging a model. We model student thinking refinement through building initial models, predicting results, testing initial models, making sense of results, debugging and retesting models, observing final models, and explaining results. We demonstrate how one student’s thinking shifted after exploring our computational microworld. We end with a discussion of microworld design features and how to implement instructional intervention in the middle school science.