In the future development of nuclear energy, the graphite-moderated helium-cooled reactors may play an important role because of their valuable technical advantages: passive safety, low cost, flexibility in the choice of fuel, high conversion energy efficiency, high burnup, more resistant fuel cladding, and low power density. General Atomics possesses a long experience with this type of reactor, and it has recently developed the gas turbine-modular helium reactor (GT-MHR), a design where the nuclear power plant is structured into four reactor modules of 600 MW(thermal). Amid its benefits, the GT-MHR offers a rather large flexibility in the choice of fuel type; Th, U, and Pu may be used in the manufacture of fuel with some degrees of freedom. As a consequence, the fuel management may be designed for different objectives aside from energy production, e.g., the reduction of actinide waste production through a fuel based on thorium. In our previous studies we analyzed the behavior of the GT-MHR with a plutonium fuel based on light water reactor (LWR) waste; in the present study we focused on the incineration of military Pu. This choice of fuel requires a detailed numerical modeling of the reactor since a high value of keff at the beginning of the reactor operation requires the modeling both of control rods and of burnable poison; by contrast, when the GT-MHR is fueled with LWR waste, at the equilibrium of the fuel composition, the reactivity swing is small.