The dynamical phenomenon of cyclic variability in combustion governed by autoignition in homogeneous charge compression ignition engines with large amounts of residual gases is investigated. A novel model is derived with two states that capture the coupling between engine cycles due to the thermal energy in the recycled residual gases and the recycled chemical energy in the unburned fuel. With the parameters tuned to data from a single cylinder engine at one level of residuals, the model predictions agree well with the experimental observations of decreasing residuals, which are associated with later phasing and increasing cyclic variability approaching misfire. A stability analysis of the model with respect to the amount of recycled residual gases shows how instabilities develop and that the dynamic behavior of the combustion phasing from cycle to cycle is stable for a range of residual gas fractions. The model and analysis offers an explanation for the experimentally observed cycle-tocycle variability, and provides a foundation for further analysis as well as development of controls mitigating the variability.