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Concerning the national biofuel policies in India, increasing plant-based fuels and lowering the use of fossil diesel in CI engines reduces the burden on foreign exchange and carbon footprints in the environment, which helps achieve “net-zero carbons emissions.” In this present study, Mahua biodiesel (BD) was used here as an ignition energy source, and CNG/ethanol (Et) was used here as the primary energy source replacing the biodiesel with a significant energy share during the combustion process. The effects of various injection and reactivity phasing strategies on a diesel engine’s combustion characteristics has been evaluated here. However, effect of this combustion characteristics on the corresponding performance and emission has also been evaluated here. This study revealed the ignition delay (ID) and combustion duration (CD) trade-off for almost every combustion phase achieved here during the testing. This analysis also incorporates the widespread effect of combustion characteristics on the performance and emission behavior of the diesel engine for both types of fuel combinations, that is, CNG + BD and Et + BD operation. For example, the lowest ID for CNG enriched combustion was 26.62% greater than ethanol enriched combustion, signifying that the ethanol delayed the start of ignition at polit-main angle of 35°-05° CA. Hence, NHC, PM, and CO2 emissions registered a lower footprint for CNG-BD operation, while ethanol-BD mode reported lower CO emission. However, ethanol-enriched combustion registered a 31.25% higher maximum CD than CNG-coupled operation, signifying a more extended period of energy release. CNG-BD operation also observed lower NHC, CO, and CO2 footprint corresponding to maximum combustion duration, and ethanol-BD mode reported lower PM emission.