This paper investigates the exergy and energy rationality of a near-future, two-step hydrogen production system in the Black Sea on a custom-built hydrogen ship with 100% onboard wind, wave, and solar energy system. In the first step of this concept, hydrogen will be produced from the low-salinity seawater by electrolysis utilizing the onboard renewable energy. Part of the hydrogen produced will be used in the second step, which is the major production step, claiming the H2S gas, which is exceptionally rich in the seawater. The hydrogen and sulfur products will be shipped by hydrogen-powered shuttle ships to the nearby city of Sinop to blend hydrogen with the natural gas (NG) to form a hydrogen city. Thus this project presents a novel coupling of the land-side and the sea-side operations with renewable energy and hydrogen in an exergy-based minimum CO2 emissions responsibilities. This on-board H2S exploration concept for hydrogen and sulfur production is compared with the current NG explorations in the Black Sea and the use of NG on the landside. A detailed comparison of the total carbon footprint shows that NG explorations in the Black Sea will be responsible for direct and indirect-nearly avoidable (due to exergy destructions) CO2 emissions, while the ever-increasing H2S threat faced by all Black Sea countries will remain at an increasing rate. A new exergy-based optimum H2S claim depth calculation and control algorithm for onboard operations have also been developed and designed, which shows that economy-based optimization—if ever exists—will be responsible for nearly avoidable CO2 emissions, while the on-board hydrogen production and utilization on the land side have a minimal environmental footprint. None of the earlier studies available in the literature concerning the exact harmful effects of hydrocarbons address exergy rationality. Renewable energy systems like wind turbines and solar energy systems, along with other renewable and waste energy systems like geothermal and wave energy are mostly treated individually, which are not free from large exergy destructions. Therefore, future energy plans with environmental concerns must be carried out from the source to the very last point of demand sectors. This is the specific attribute of this research. Novelty Statement None of the studies about the exact harmful effects of hydrocarbons involve exergy rationality and the consequences of this ignorance on the environment and overall energy budget and economy. Renewable energy systems like wind turbines and solar energy systems, along with other renewable and waste energy systems like geothermal and wave energy are mostly treated individually, which are not free from exergy destructions. For example, a solar photovoltaic (PV) plant generates power but releases heat back without claiming it. This unclaimed heat represents about 50% of the unit exergy of the available solar energy and leads to exergy destruction that is responsible for nearly avoidable CO2 emissions because destroyed thermal exergy has to be offset by spending additional fuel in another system, which most likely is using fossil fuels in a boiler. The term nearly precedes the word avoidable, because exergy destructions may not be completely avoided. Even solar and wind energy systems have exergy destruction components during their operation. Yet, a solar PV and heat system would be a much better choice from the exergy rationality point of view. Although the ongoing increase in the renewable shares in the energy stock, it is essential to follow where the power is used in the built environment. For example, according to Global Wind Energy Council, within the next 10 years 234 GW, within the next 30 years 1400 GW offshore wind power capacity is expected to be installed. However, these installations will never know where this electricity and how this electricity is used in an energy/exergy balance and rationality when coupled to the landside through national and international grids. Therefore, future energy plans with environmental concerns must be carried out from the source to the very last point of demand sectors. Whether off-shore or land-based, wind turbines just generate electric power without asking where the electricity goes and how rational it is used in the built environment. There is no control over the best way of utilizing this wind energy. Instead, hydrogen production with renewables and utilization in next-generation fuel cells produces power and heat (pending on heat distribution tariffs for the fifth-generation district energy systems and LowEx applications, the temperature is the best fit for LowEx applications). The interrupted and unpredictable characteristics of renewables are offset by hydrogen storage.