The intent of this FOA is to identify, evaluate, and select innovative pilot- or demonstration-scale integrated biorefineries that can produce hydrocarbon fuels that meet military specifications for JP-5 (jet fuel primarily for the Navy), JP-8 (jet fuel primarily for the Air Force), or F-76 (diesel). Integrated biorefineries proposed for this funding opportunity may employ various combinations of feedstocks and conversion technologies to produce a variety of products, but the primary focus must be on producing biofuels. Novel and highly innovative technologies are strongly encouraged. Topic Area 1 requests applicants to design, construct and/or operate an integrated pilot- or demonstration-scale integrated biorefinery in order to validate the proposed technology using an acceptable lignocellulosic or waste-based feedstock, to produce an acceptable biofuel. Processes are also eligible under this topic that can utilize advanced technology approaches for the efficient conversion of carbon dioxide (CO2) (rather than direct conversion of lignocellulosic biomass) directly to liquid transportation fuels. Topic Area 2 requests applicants to design, construct and/or operate an integrated pilot- or demonstration-scale integrated biorefinery in order to validate the proposed technology using an acceptable algal type feedstock, to produce an acceptable biofuel.