A fuel cell system with a fuel cell having an anode adapted to receive fuel and a cathode adapted to receive oxidant, an anode oxidizing assembly adapted to receive output of said anode and input oxidant and to output oxidant gas for said cathode, a fuel supply assembly including a first fuel flow control part, said fuel supply assembly being adapted to supply fuel to said anode at a flow rate that is equal to or less than a first flow rate, and a low flow bypass assembly which, upon the occurrence of a first condition of said fuel cell system, causes fuel supplied by said fuel supply part to bypass said first fuel flow control part and flow through said low flow bypass assembly so as to limit the flow rate of fuel being supplied to a second flow rate smaller than said first flow rate.