The spin state transition in LaCoO3 has eluded description for decades despite concerted theoretical and experimental effort. In this study, we approach this problem using fully charge self-consistent Density Functional Theory + Embedded Dynamical Mean Field Theory (DFT+DMFT). We show from first principles that LaCoO3 cannot be described by a single, pure spin state at any temperature. Instead, we observe a gradual change in the population of higher spin multiplets with increasing temperature, with the high spin multiplets being excited at the onset of the spin state transition followed by the intermediate spin multiplets being excited at the metal insulator transition temperature. We explicitly elucidate the critical role of lattice expansion and oxygen octahedral rotations in the spin state transition. We also reproduce, from first principles, that the spin state transition and the metal-insulator transition in LaCoO3 occur at different temperature scales. In addition, our results shed light on the importance of electronic entropy in driving the spin state transition, which has so far been ignored in all first principles studies of this material.