Whether four-stroke or two-stroke, marine engines are an essential component of ships as they are the main source of power and, at the same time, the primary source of pollution. Therefore, the main concern of the industry is to improve engine performance and reduce exhaust emissions. Marine diesel engines have shown a great revolution these years towards decarbonisation and reduction of fuel consumption to fit the market needs. The simulation software developed varying from 0D models to 3D models, is a good support for the studies to support design changes, particularly in the development of fuel flex engines. The concept of a dual-fuel engine became widely used, which supports the use of alternative fuels as the main fuels with a small quantity of diesel oil as possible fuel. A system-level approach is used to evaluate the trade-offs and efficiency potential of the full system. Different comparative studies and sensitivity analyses are to be performed to find the optimal plan layout along the engine load diagram to reduce the initial and operating costs and ensure the best fulfilment of the vessel needs regarding mechanical, fluid and thermal energies. Different surrogate models based on response surface methodology (RSM) are used from the optimised results to define the performance of different selected components to be further used without performing the time-consuming simulation of all the complex physical processes. On the other hand, fuel cells as an alternative propulsion system can achieve higher efficiencies than conventional internal combustion machines, especially with the bottoming cycle. Therefore, it is important to investigate the integration of various bottoming cycles of fuel cells, especially solid oxide fuel cells (SOFC) and molten carbonate fuel cell (MCFC), and their use in ships. In addition to alternative fuels such as hydrogen, methanol, and ammonia, these types of cells can use conventional fuels used in ships directly or in a reformed form. Thus, achieving zero or near-zero CO2 emission targets on ships may be possible. The fuel cells are electrochemically and thermodynamically modelled and integrated into the various bottoming cycles for ships. Integrated systems’ models are simulated, and energy, exergy, economy, and environment (4E) analyses are carried out. According to the results of the 4E analysis, the most suitable fuel cell operating temperature, current density, and operating time parameters due to cell degradation are determined and the effect of the losses in the fuel cell depending on the current density change is examined for the suitable operating conditions. Finally, the 4E analysis results of the proposed system are compared with the results obtained for different alternative fuels. Significant efficiency gains and emission reductions can be achieved by replacing conventional direct drive mechanical transmission systems with either hybrid or complete electrical transmission the “allelectric ship”. The use of electric transmission removes the “tyranny of the shaft line” and permits a more flexible machinery layout and engine operation making it easier to avoid low load running which is inefficient and more polluting. Electric transmission opens up the opportunity for energy storage systems such as batteries to load level and further reduce emissions. Different main machinery configurations will be investigated to compare their ship impact and performance when operating on different fuel types.