In this work, the phenomenon of cycle -to -cycle variability (CCV) of combustion in a spark ignition engine is investigated to give a deeper understanding of CCV generation. The main objective is to localize within the cylinder and all along the engine cycle the flow variabilites and identify some driving mechanisms originating in the flow structures and leading to combustion variabilites. In Part I , the application of empirical mode decomposition methods combined with topology -based techniques to the LES flow results allowed the extraction of the large-scale flow motion from the small-scale turbulence and the follow-up of their evolution during compression stroke [1]. A link was then established between the combustion process and the tumble formation and destabilization near BDC. In the present paper, the overall tumble motion development during compression and intake strokes is quantitatively analyzed, and links are built between different engine phases to establish the cause -and -effect chain. Other CCV factors, such as spray injection and exhaust gas recirculation, were not included in the current study. However, the developed methodology for in -cylinder flow analysis could be used in studies on other engine configurations to improve the development of engine designs. Novelty and significance statement In this work, the cycle -to -cycle variability (CCV) of combustion in a spark ignition engine is investigated to give a deeper understanding of CCV generation. The present study focuses on CCV caused by the stochastic nature of internal turbulent flow structures. LES approach is chosen due to its ability to capture CCV, and advanced flow analysis tools are developed and applied to LES results to characterize instantaneous flow structures of different scales in the three-dimensional domain and separately quantify their impacts on combustion. A first important finding is that flow -wall interactions near BDC determine the tumble evolution. A second novelty is the characterization of several 3D dominant flow interactions during intake yielding large-scale flow variability. A third novelty and important finding is that links are found between the flow organization during intake, the tumble development, and destabilization during early compression and the combustion. Throughout our analyses starting from the spark timing and going back to the early intake phase, a cause -and -effect chain is finally established between the development of in -cylinder flow and the combustion variability.