NOVELTY - A fuel cell electric power generation system comprises (a) a fuel processing subsystem containing an autothermal reformer, (b) a hydrogen separator, (c) a fuel cell stack, (d) a burner and (e) a carbon dioxide scrubber.    USE - In submarines (claimed), for use in stationary electric power generation application, vehicular applications such as surface ships, trains and industrial and heavy-duty vehicles.    ADVANTAGE - The system is capable of operating easily and efficiently using diesel as a fuel to convert the fuel to a hydrogen-rich reformate stream. Autothermal reforming combines catalytic partial oxidation and steam reforming, and the system uses the exothermic combustion reactions to drive the endothermic reforming reaction. At the high operating temperatures typical of autothermal reformers, sulfur in the fuel is converted to H2S, which does not significantly poison the catalyst and permits downstream sulfur removal. This may result in a simpler fuel processing system, as a hydrodesulfurizer (HDS) is not required. Compared to fuel processing systems employing steam reformers, start-up times also tend to be shorter due to the heat supplied to the catalyst bed by catalytic combustion. The system makes more efficient use of the oxygen stored on-board when used as an air-independent propulsion system.    DETAILED DESCRIPTION - A fuel cell electric power generation system comprises: (a) a fuel processing subsystem containing autothermal reformer for converting a fuel stream to a reformate stream comprising hydrogen, (b) a hydrogen separator fluidly connected to and located downstream of the fuel processing subsystem for receiving the reformate stream, (c) a fuel cell stack comprising at least one fuel cell fluidly connected to receive an oxidant stream and hydrogen-rich stream from the hydrogen separator, (d) a burner fluidly connected to receive and to combust the raffinate stream to produce a burner outlet stream containing carbon dioxide and oxygen and (e) a carbon dioxide scrubber fluidly connected to receive the burner outlet stream for removing at least a portion of the carbon dioxide and for recovering at least a portion of the oxygen from the burner outlet stream and supplying an oxygen-containing stream to the burner. The separator comprises a membrane for separating the reformate stream into a hydrogen-rich stream and a raffinate stream.    An INDEPENDENT CLAIM is also included for operating the system by    (i) catalytically reforming the fuel stream in an autothermal reformer to produce the reformate stream,    (ii) separating the reformate stream into a pure hydrogen stream and raffinate stream in the hydrogen separator,    (iii) supplying the hydrogen stream and an oxidant stream from an oxidant supply to the fuel cell stack, producing anode and cathode exhaust streams from hydrogen and oxidant streams respectively and electrical power,    (iv) combusting the raffinate stream in the burner to produce heat and the burner outlet stream,    (v) supplying the burner outlet stream to the carbon dioxide scrubber via a burner stream inlet. The scrubber comprises a stream inlet, a water discharge stream outlet and a gas recovery outlet. Carbon dioxide is dissolved in water stream and the oxygen-containing gas steam is produced, and    (vi) supplying the oxygen-containing gas stream to the burner.