Diesel fuel is a primary candidate for use aboard submarines. It has a high energy density and it is already in the Navy inventory. Fuel cells are attractive for submarines from an energy density perspective. Unfortunately, in hydrocarbon reforming power systems, the fuel cell power density is overshadowed by the fuel processing system which is often several times the size and cost of the fuel cell. The system complexity decreases efficiency. Hydrocarbon reformate contains unacceptable amounts of impurities, such as carbon oxides and ammonia, which have been shown to adversely affect the life of PEM cells. Diesel fuel reformate has a low hydrogen concentration resulting in large shift converters and selective oxidizers. The Clean Gas Reformer (CGR) addresses the deficiencies of conventional fuel processors and integrates efficiently with a PEM fuel cell. The CGR combines an ATR with a novel hydrogen separator - glass - resulting in fuel cell reactant gas that is clean and 100% hydrogen, increasing performance, lifetime and reliability. Based on MEMS technology, the ATR is a simple, reliable method of generating syngas from diesel fuel. The CGR supplies pure hydrogen to the fuel cell