Understanding the role of the phase transitions during lithiation and delithiation of graphite remains a problem of fundamental importance, but also practical relevance owing to its widespread use as the anode material in most commercial lithium-ion cells. Previously performed density functional theory (DFT) calculations show a rapid change in the lithium-carbon interaction at low occupation, due to partial charge transfer from Li to C. We integrate this effect in our previously developed two level mean field model, which describes the Stage I – Stage II transition in graphite. The modified model additionally describes the most predominant transition that occurs at low Li content in graphite, which results in a previously unexplained feature in voltage and dQ/dV profiles, and thermodynamic measurements of partial molar enthalpy. In contrast with the Stage I-Stage II transition, this extra feature is not associated with observable features in the partial molar entropy and our model demonstrates why. There is a sharp change in the open circuit voltage at very low Li occupation, followed by a transition to a voltage plateau (peak in dQ/dV). The behaviour arises due to the contrasting effects of the partial molar entropy and enthalpy terms on the partial molar Gibbs energy and hence cell voltage. Hence the voltage profile and phase transitions can be approximated for all lithium occupations, potentially allowing a predictive capability in cell level models.