To achieve future targets for reducing greenhouse-gas and pollutant emissions from internal combustion engines, alternative fuels as well as alternative combustion modes offer great potential. The simultaneous use of two different fuels offers additional degrees of freedom to realize highly efficient and low-emission combustion, but also poses further challenges. To this end, this paper presents the Molecularly-Controlled high swirl Combustion system, MCC, which involves dual direct injection of a low- and a high-reactivity fuel in combination with lean relative air-fuel-ratios, high compression ratio, and compression ignition. The principle centers on the generation of a strong “molecular spark” – a spacially confined area in the combustion chamber where the reactivity of the fuel mixture is sufficient to form a robust, controllable ignition source. Subsequently, combustion spreads to the rest of the combustion chamber. Ethanol was used as the low-reactivity fuel and 1-octanol or conventional diesel fuel as the high-reactivity fuel to investigate the combustion characteristics, efficiency, and raw emission potential under various operating conditions with a light-duty single-cylinder research engine. The results are compared with compression ignition operation of conventional diesel fuel and neat 1-octanol. The MCC system achieves a large reduction in soot-emissions, even at very low NOx-levels below 0.1 g/kWh and a considerable increase in indicated efficiency over conventional compression ignition combustion.