Fuel transition can decarbonize shipping and help meet IMO 2050 goals. In this paper, HFO with CCS, LNG with CCS, bio-methanol, biodiesel, hydrogen, ammonia, and electricity were studied using empirical ship design models from a fleet-level perspective and at the Tank-To-Wake level, to assist operators, technology developers, and policy makers. The cargo attainment rate CAR (i.e., cargo that must be displaced due to the low-C propulsion system), the ES (i.e., TTW energy needed per ton*n.m.), the CS (economic cost per ton*n.m.), and the carbon intensity index CII (gCO2 per ton*n.m.) were calculated so that the potential of the various alternatives can be compared quantitatively as a function of different criteria. The sensitivity of CAR towards ship type, fuel type, cargo type, and voyage distance were investigated. All ship types had similar CAR estimates, which implies that considerations concerning fuel transition apply equally to all ships (cargo, containership, tankers). Cargo type was the most sensitive factor that made a ship either weight or volume critical, indirectly impacting on the CAR of different fuels; for example, a hydrogen ship is weight-critical and has 2.3% higher CAR than the reference HFO ship at 20,000 nm. Voyage distance and fuel type could result in up to 48.51% and 11.75% of CAR reduction. In addition to CAR, the ES, CS, and CII for a typical mission were calculated and it was found that HFO and LNG with CCS gave about 20% higher ES and CS than HFO, and biodiesel had twice the cost, while ammonia, methanol, and hydrogen had 3−4 times the CS of HFO and electricity about 20 times, suggesting that decarbonisation of the world’s fleet will come at a large cost. As an example of including all factors in an effort to create a normalized scoring system, an equal weight was allocated to each index (CAR, ES, CS, and CII). Biodiesel achieved the highest score (80%) and was identified as the alternative with the highest potential for a deep-seagoing containership, followed by ammonia, hydrogen, bio-methanol, and CCS. Electricity has the lowest normalized score of 33%. A total of 100% CAR is achievable by all alternative fuels, but with compromises in voyage distance or with refuelling. For example, a battery containership carrying an equal amount of cargo as an HFO-fuelled containership can only complete 13% of the voyage distance or needs refuelling seven times to complete 10,000 n.m. The results can guide decarbonization strategies at the fleet level and can help optimise emissions as a function of specific missions.