The relative combustion phasing of a homogenous charge compression ignition engine is controlled by controlling the introduction of ions and free radicals to cylinders in the engine. The engine has an engine housing with at least a first and second cylinder and an intake system that introduces a combustible mixture of air and fuel to the cylinders. A piston is disposed in each of the cylinders and is operable to compress a combustible mixture until the mixture auto ignites, without the introduction of a spark.