This chapter examines three principal theories of eukaryogenesis and elucidates why the transition from prokaryotes to eukaryotes constitutes a major evolutionary transition, as defined by Maynard-Smith and Szathmáry. It argues that these theories, alongside Maynard-Smith and Szathmáry’s framework, offer intriguing insights into this evolutionary process, which remains an enigma. From a philosophical perspective, eukaryogenesis challenges our understanding of how new biological organisations attain a sufficient degree of functional integration to become autonomous, physiological, and evolutionary individuals. Therefore, the concept of functional integration is central to comprehending eukaryogenesis.