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This dissertation proposes an exploration of a variety of themes in philosophy of science through the lens of a case study in evolutionary biology. It draws from a careful analysis and comparison of the hypotheses from Bill Martin and Tom Cavalier-Smith. These two scientists produced contrasted and competing accounts for one of the main events in the history of life, the origin of eukaryotic cells. This case study feeds four main philosophical themes around which this dissertation is articulated. (1) Theorizing: What kind of theory are hypotheses about unique events in the past? (2) Representation: How do hypotheses about the past represent their target? (3) Evidential claims: What kind of evidence is employed and how do they constrain these hypotheses? (4) Pluralism: What are the benefits and the risks associated with the coexistence of rival hypotheses? This work both seeks to rearticulate traditional debates in philosophy of science in the light of a lesser-known case of scientific practice and to enrich the catalogue of existing case studies in the philosophy of historical sciences.