The aim of this study is to parametrically investigate the effects of varying alternative fuel usage, ship cruising duration and parallel generator combinations on exhaust emissions, EEXI and CII values in the cargo ships. In the study the generators were parallelized to provide 48% load for each combination and parametric studies were performed for the 75% load condition of the main engine. Flue gas products for each fuel were determined by the chemical kinetics method. It has been observed that emissions in the case of single generator use decrease compared to the parallel generator use case. Increasing ship cruising duration caused the EEXI value and CII index to decrease by approximately 2.5%. It has been determined that CII is at C rating for the most widely utilized medium term alternative fuels and A rating for ammonia and hydrogen for long-term net-zero targets. In conclusion, the study provides critical data to inform the current debate on the potential use of alternative fuels in relation to IMO ' s current strategies to reduce carbon emissions from ships in the long and medium term.