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This paper investigates flow and combustion in a full-cycle simulation of a four-stroke, three-valve HCCI engine by visualizing the flow with pathlines. Pathlines trace massless particles in a transient flow field. In addition to visualization, pathlines are used here to trace the history, or evolution, of flow fields and species. In this study evolution is followed from the intake port through combustion. Pathline analysis follows packets of intake charge in time and space from induction through combustion. The local scalar fields traversed by the individual packets in terms of velocity magnitude, turbulence, species concentration and temperatures are extracted from the simulation results. The results show how the intake event establishes local chemical and thermal environments in-cylinder and how the species respond (chemically react) to the local field.