This paper outlines the development of a comprehensive numerical framework for the partially stratified charge (PSC) lean-burn natural gas engine. A 3D model of the engine was implemented to represent fluid motion and combustion. The spark ignition model was based on the works of Herweg and Maly (1992, “A Fundamental Model for Flame Kernel Formation in SI Engines,” SAE Technical Publication, Paper No. 922243) and Tan and Reitz (2006, “An Ignition and Combustion Model Based on the Level-Set Method for Spark Ignition Engine Multidimensional Modeling,” Combust. Flame, 145, pp. 1–15). The EDC model (Ertesvåg and Magnussen, 2000, “The Eddy Dissipation Turbulence Energy Cascade Model,” Combust. Sci. Technol., 159, pp. 213–235) with a two-step mechanism was used to model natural gas turbulent combustion process. An open geometry simulation strategy was adopted to account for intake-exhaust gas and valve movements. Each simulation was executed for multiple cycles to produce a representative residual gas fraction. The numerical results were compared with the experimental data obtained on the Ricardo Hydra single cylinder research engine for both homogeneous and PSC cases and they were found to be in excellent agreement in pressure trace and heat release rate. The detailed investigation of the numerical data showed the development of an ignitable mixture under PSC cases, allowing stable kernel growth well beyond the lean misfire limit of the bulk mixture. Furthermore, limits on successful ignition can be identified using the ignition model, which exhibited self-similar behavior in terms of flame speed and turbulent fluctuation. It can also be shown that, at ultralean air-fuel ratios, the PSC plume helps replicate the ignition conditions that can be found under stoichiometric operation.