One aspect of the invention relates to a clean power generation system in which an internal combustion engine is operated to produce shaft power and an exhaust stream. The exhaust stream is processed by a fuel cell. Fluctuations in power demand are met, at least in part, by increasing or decreasing power output from the fuel cell and/or power uptake or output from a power storage device. The engine can operate at a relatively constant rate, providing a steady exhaust stream, which facilitates pollution control and fuel cell operation. According to another aspect of the invention, the exhaust of an engine is treated with a fuel cell having an electrolyte that conducts protons. In addition to removing pollutants from the exhaust while generating useful power, the fuel cell can provide a supply of low acidity water. The water can be used in the fuel reformer.